@article{Ercsey-Ravasz2011,
annote = {Analysis of k-SAT as a continuous dynamical system.  Shows that fluctuations in the energy function increase exponentially with the hardness of the problem instance.},
author = {Ercsey-Ravasz, M\'{a}ria and Toroczkai, Zolt\'{a}n},
doi = {10.1038/nphys2105},
file = {:Users/rnowling/Documents/Mendeley Desktop/Ercsey-Ravasz, Toroczkai/2011/Optimization hardness as transient chaos in an analog approach to constraint satisfaction/Ercsey-Ravasz, Toroczkai - 2011 - Optimization hardness as transient chaos in an analog approach to constraint satisfaction.pdf:pdf},
issn = {1745-2473},
journal = {Nature Physics},
keywords = {Annotated},
mendeley-tags = {Annotated},
month = oct,
number = {10},
pages = {1--5},
publisher = {Nature Publishing Group},
title = {{Optimization hardness as transient chaos in an analog approach to constraint satisfaction}},
url = {http://www.nature.com/doifinder/10.1038/nphys2105},
volume = {7},
year = {2011}
}
@article{Labute2010,
abstract = {We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is based on perturbing an existing conformation along a molecular dynamics trajectory using initial atomic velocities with kinetic energy concentrated on the low-frequency vibrational modes, followed by energy minimization. A novel Chebyshev polynomial filter is used to heavily dampen the high-frequency components of a randomly generated Maxwell-Boltzmann velocity vector. The method is very efficient, even for large systems; it is straightforward to implement and requires only standard force-field energy and gradient evaluations. The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks.},
author = {Labute, Paul},
doi = {10.1021/ci900508k},
file = {:Users/rnowling/Documents/Mendeley Desktop/Labute/2010/LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops/Labute - 2010 - LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops.pdf:pdf},
issn = {1549-960X},
journal = {Journal of chemical information and modeling},
keywords = {Animals,Cattle,Macrocyclic Compounds,Macrocyclic Compounds: chemistry,Molecular Conformation,Molecular Dynamics Simulation,Molecular Dynamics Simulation: economics,Protein Conformation,Proteins,Proteins: chemistry,rho-Associated Kinases,rho-Associated Kinases: chemistry},
month = may,
number = {5},
pages = {792--800},
pmid = {20429574},
title = {{LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20429574},
volume = {50},
year = {2010}
}
@article{Li2004,
abstract = {The structural flexibilities of two molecular machines, myosin and Ca(2+)-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion functions. The normal mode analysis with physical intermolecular interactions was made possible by an improved implementation of the block normal mode (BNM) approach. The BNM results clearly illustrated that the large-scale conformational transitions implicated in the functional cycles of the two motor systems can be largely captured with a small number of low-frequency normal modes. Therefore, the results support the idea that structural flexibility is an essential part of the construction principle of molecular motors through evolution. Such a feature is expected to be more prevalent in motor proteins than in simpler systems (e.g., signal transduction proteins) because in the former, large-scale conformational transitions often have to occur before the chemical events (e.g., ATP hydrolysis in myosin and ATP binding/phosphorylation in Ca(2+)-ATPase). This highlights the importance of Brownian motions associated with the protein domains that are involved in the functional transitions; in this sense, Brownian molecular machines is an appropriate description of molecular motors, although the normal mode results do not address the origin of the ratchet effect. The results also suggest that it might be more appropriate to describe functional transitions in some molecular motors as intrinsic elastic motions modulating local structural changes in the active site, which in turn gets stabilized by the subsequent chemical events, in contrast with the conventional idea of local changes somehow getting amplified into larger-scale motions. In the case of myosin, for example, we favor the idea that Brownian motions associated with the flexible converter propagates to the Switch I/II region, where the salt-bridge formation gets stabilized by ATP hydrolysis, in contrast with the textbook notion that ATP hydrolysis drives the converter motion. Another useful aspect of the BNM results is that selected low-frequency normal modes have been identified to form a set of collective coordinates that can be used to characterize the progress of a significant fraction of large-scale conformational transitions. Therefore, the present normal mode analysis has provided a stepping-stone toward more elaborate microscopic simulations for addressing critical issues in free energy conversions in molecular machines, such as the coupling and the causal relationship between collective motions and essential local changes at the catalytic active site where ATP hydrolysis occurs.},
annote = {Validation of BNM method through analysis of Myosin-II and Ca-ATPase},
author = {Li, Guohui and Cui, Qiang},
doi = {10.1016/S0006-3495(04)74152-1},
file = {:Users/rnowling/Documents/Mendeley Desktop/Li, Cui/2004/Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach myosin-II and Ca2 -ATPase/Li, Cui - 2004 - Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach myosin-II and Ca2 -ATPase.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Algorithms,Annotated,Binding Sites,Calcium-Transporting ATPases,Calcium-Transporting ATPases: chemistry,Diagonalization,Diffusion,Elasticity,Molecular Motor Proteins,Molecular Motor Proteins: chemistry,Motion,Myosin Type II,Myosin Type II: chemistry,NMA,Protein Binding,Protein Conformation},
mendeley-tags = {Annotated,Diagonalization,NMA},
month = feb,
number = {2},
pages = {743--63},
pmid = {14747312},
publisher = {Elsevier},
title = {{Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1303924\&tool=pmcentrez\&rendertype=abstract},
volume = {86},
year = {2004}
}
@article{Li2002,
abstract = {A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically reduces the size of the matrix involved in diagonalization. In the current work, by constructing the atomic hessian elements required in the projection operation on the fly, the memory requirement for the BNM approach has been significantly reduced from that of standard normal mode analysis and previous implementation of BNM. As a result, low frequency modes, which are of interest in large-scale conformational changes of large proteins or protein-nucleic acid complexes, can be readily obtained. Comparison of the BNM results with standard normal mode analysis for a number of small proteins and nucleic acids indicates that many properties dominated by low frequency motions are well reproduced by BNM; these include atomic fluctuations, the displacement covariance matrix, vibrational entropies, and involvement coefficients for conformational transitions. Preliminary application to a fairly large system, Ca(2+)-ATPase (994 residues), is described as an example. The structural flexibility of the cytoplasmic domains (especially domain N), correlated motions among residues on domain interfaces and displacement patterns for the transmembrane helices observed in the BNM results are discussed in relation to the function of Ca(2+)-ATPase. The current implementation of the BNM approach has paved the way for developing efficient sampling algorithms with molecular dynamics or Monte Carlo for studying long-time scale dynamics of macromolecules.},
annote = {Describes more memory-efficient version of RTB method where Hessian values are computed as needed rather than all at once and stored.},
author = {Li, Guohui and Cui, Qiang},
doi = {10.1016/S0006-3495(02)75257-0},
file = {:Users/rnowling/Documents/Mendeley Desktop/Li, Cui/2002/A coarse-grained normal mode approach for macromolecules an efficient implementation and application to Ca(2)-ATPase/Li, Cui - 2002 - A coarse-grained normal mode approach for macromolecules an efficient implementation and application to Ca(2)-ATPase.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Algorithms,Annotated,Binding Sites,Biophysical Phenomena,Biophysics,Calcium,Calcium-Transporting ATPases,Calcium-Transporting ATPases: chemistry,Calcium-Transporting ATPases: metabolism,Calcium: chemistry,Calmodulin,Calmodulin: chemistry,Cytoplasm,Cytoplasm: metabolism,Diagonalization,Entropy,Hydrolysis,Models,Monte Carlo Method,NMA,Phosphorylation,Protein Binding,Protein Conformation,Protein Structure,Secondary,Statistical,Temperature,Tertiary,Time Factors},
mendeley-tags = {Annotated,Diagonalization,NMA},
month = nov,
number = {5},
pages = {2457--74},
pmid = {12414680},
publisher = {Elsevier},
title = {{A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302332\&tool=pmcentrez\&rendertype=abstract},
volume = {83},
year = {2002}
}
@article{Tama2000,
abstract = {Normal mode analysis of proteins of various sizes, ranging from 46 (crambin) up to 858 residues (dimeric citrate synthase) were performed, by using standard approaches, as well as a recently proposed method that rests on the hypothesis that low-frequency normal modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino-acid residues. Such a hypothesis is strongly supported by our results, because we show that the latter method, named RTB, yields very accurate approximations for the low-frequency normal modes of all proteins considered. Moreover, the quality of the normal modes thus obtained depends very little on the way the polypeptidic chain is split into blocks. Noteworthy, with six amino-acids per block, the normal modes are almost as accurate as with a single amino-acid per block. In this case, for a protein of n residues and N atoms, the RTB method requires the diagonalization of an n x n matrix, whereas standard procedures require the diagonalization of a 3N x 3N matrix. Being a fast method, our approach can be useful for normal mode analyses of large systems, paving the way for further developments and applications in contexts for which the normal modes are needed frequently, as for example during molecular dynamics calculations.},
annote = {Describes Rotation, Translation Block (RTB) method for approximating normal modes as rotations and translations of blocks of residues.  FIrst, residues are organized into blocks and 3 rotation and 3 translation eigenpairs in reduced space are found.  Secondly, Hessian is projected onto reduced space and diagonalized to obtain reduced-space normal modes.  And lastly, reduced-space normal modes are projected back onto full space.  Use of high-frequency modes or perturbation-iteration scheme were dropped from Durand94.},
author = {Tama, F and Gadea, F X and Marques, O and Sanejouand, Y H},
file = {:Users/rnowling/Documents/Mendeley Desktop/Tama et al/2000/Building-block approach for determining low-frequency normal modes of macromolecules/Tama et al. - 2000 - Building-block approach for determining low-frequency normal modes of macromolecules.pdf:pdf},
issn = {0887-3585},
journal = {Proteins},
keywords = {Algorithms,Annotated,Diagonalization,NMA,Protein Conformation,Proteins,Proteins: chemistry},
mendeley-tags = {Annotated,Diagonalization,NMA},
month = oct,
number = {1},
pages = {1--7},
pmid = {10944387},
title = {{Building-block approach for determining low-frequency normal modes of macromolecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10944387},
volume = {41},
year = {2000}
}
@article{Pomes1990,
author = {Pom\`{e}s, R. and McCammon, J.A.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Pom\`{e}s, McCammon/1990/Mass and Step Length Optimization For the Calculation of Equilibrium Properties by Molecular Dynamics Simulation/Pom\`{e}s, McCammon - 1990 - Mass and Step Length Optimization For the Calculation of Equilibrium Properties by Molecular Dynamics Simulation.pdf:pdf},
journal = {Chemical Physics Letters},
number = {4},
pages = {425--428},
publisher = {Elsevier},
title = {{Mass and Step Length Optimization For the Calculation of Equilibrium Properties by Molecular Dynamics Simulation}},
url = {http://www.sciencedirect.com/science/article/pii/000926149085055H},
volume = {166},
year = {1990}
}
@article{Bennett1975,
annote = {Describes replacing the diagonal mass matrix with a mass tensor designed to increae sampling efficiency by compressing the range of frequencies at which motions occur.  Suggests defining the mass matrix in terms of modified normal modes and frequencies and shows that, in the microcanonical ensemble, the probability of configurations is scaled by the determinant of the mass tensor, so defining a mass tensor with determinant 1 will not affect the probabilities.},
author = {Bennett, Charles H.},
doi = {10.1016/0021-9991(75)90077-7},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bennett/1975/Mass tensor molecular dynamics/Bennett - 1975 - Mass tensor molecular dynamics.pdf:pdf},
issn = {00219991},
journal = {Journal of Computational Physics},
keywords = {Annotated,Lightwater},
mendeley-tags = {Annotated,Lightwater},
month = nov,
number = {3},
pages = {267--279},
title = {{Mass tensor molecular dynamics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0021999175900777},
volume = {19},
year = {1975}
}
@article{Zuckerman2006,
abstract = {The replica exchange approach, also called parallel tempering, is gaining popularity for biomolecular simulation. We ask whether the approach is likely to be efficient compared to standard simulation methods for fixed-temperature equilibrium sampling. To examine the issue, we make a number of straightforward observations on how "fast" high-temperature molecular simulations can be expected to run, as well as on how to characterize efficiency in replica exchange. Although our conclusions remain to be fully established, based on a range of results in the literature and some of our own work with a 50-atom peptide, we are not optimistic for the efficiency of replica exchange for canonical sampling of biomolecules.},
author = {Zuckerman, Daniel M and Lyman, Edward},
doi = {10.1021/ct0600464},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zuckerman, Lyman/2006/A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation/Zuckerman, Lyman - 2006 - A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.pdf:pdf},
issn = {1549-9626},
journal = {Journal of chemical theory and computation},
month = jan,
number = {4},
pages = {12001202},
pmid = {19043602},
title = {{A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2586297\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2006}
}
@article{Liu2007,
abstract = {A coarse-grained representation of a condensed phase system can significantly reduce the number of system degrees of freedom, making coarse-grained simulations very computationally efficient. Moreover, coarse graining can smoothen the free energy landscape of the system. Thus coarse-grained dynamics is usually faster than its fully atomistic counterpart. In this work, the smart resolution replica exchange method is introduced that incorporates the information from coarse-grained simulations into atomistic simulations in order to accelerate the sampling of rough, complex atomistic energy landscapes. Within this methodology, interactions between particles are defined by a potential energy that interpolates between a fully atomistic potential and a fully coarse-grained effective potential according to a parameter lambda. Instead of exchanging the configurations from neighboring resolutions directly, as has been done in the resolution replica exchange methods [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006); M. Christen and W. F. v. Gunsteren, J. Chem. Phys. 124, 154106 (2006)], the configuration described at the coarser resolution is first relaxed before an exchange is attempted, similar to the smart walking method [R. Zhou and B. J. Berne, J. Chem. Phys. 107, 9185 (1997)]. This approach greatly increases the acceptance ratio of exchange and only two replicas, one at the atomistic level and one at the coarse-grained level, are usually required (although more can be implemented if desired). This new method can approximately obtain the correct canonical sampling if the exchange interval is sufficiently large to allow the system to explore the local energy landscape. The method is demonstrated for a two-dimensional model system, where the ideal population distribution can be recovered, and also for an alanine polypeptide (Ala(15)) model with explicit water, where its native structure, an alpha helix, is obtained from the extended structure within 1 ns.},
author = {Liu, Pu and Voth, Gregory a},
doi = {10.1063/1.2408415},
file = {:Users/rnowling/Documents/Mendeley Desktop/Liu, Voth/2007/Smart resolution replica exchange an efficient algorithm for exploring complex energy landscapes/Liu, Voth - 2007 - Smart resolution replica exchange an efficient algorithm for exploring complex energy landscapes.pdf:pdf},
issn = {0021-9606},
journal = {The Journal of chemical physics},
keywords = {Algorithms,Biopolymers,Biopolymers: chemistry,Computer Simulation,Energy Transfer,Models, Chemical,Models, Molecular},
month = jan,
number = {4},
pages = {045106},
pmid = {17286516},
title = {{Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17286516},
volume = {126},
year = {2007}
}
@article{Zheng2008,
abstract = {The efficiency of temperature replica exchange (RE) simulations hinge on their ability to enhance conformational sampling at physiological temperatures by taking advantage of more rapid conformational interconversions at higher temperatures. While temperature RE is a parallel simulation technique that is relatively straightforward to implement, kinetics in the RE ensemble is complicated, and there is much to learn about how best to employ RE simulations in computational biophysics. Protein folding rates often slow down above a certain temperature due to entropic bottlenecks. This "anti-Arrhenius" behavior represents a challenge for RE. However, it is far from straightforward to systematically explore the impact of this on RE by brute force molecular simulations, since RE simulations of protein folding are very difficult to converge. To understand some of the basic mechanisms that determine the efficiency of RE, it is useful to study simplified low dimensionality systems that share some of the key characteristics of molecular systems. Results are presented concerning the efficiency of temperature RE on a continuous two-dimensional potential that contains an entropic bottleneck. Optimal efficiency was obtained when the temperatures of the replicas did not exceed the temperature at which the harmonic mean of the folding and unfolding rates is maximized. This confirms a result we previously obtained using a discrete network model of RE. Comparison of the efficiencies obtained using the continuous and discrete models makes it possible to identify non-Markovian effects, which slow down equilibration of the RE ensemble on the more complex continuous potential. In particular, the rate of temperature diffusion and also the efficiency of RE is limited by the time scale of conformational rearrangements within free energy basins.},
author = {Zheng, Weihua and Andrec, Michael and Gallicchio, Emilio and Levy, Ronald M},
doi = {10.1021/jp076377+},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zheng et al/2008/Simple continuous and discrete models for simulating replica exchange simulations of protein folding/Zheng et al. - 2008 - Simple continuous and discrete models for simulating replica exchange simulations of protein folding.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
keywords = {Computer Simulation,Kinetics,Models, Biological,Probability,Protein Folding,Proteins,Proteins: chemistry,Proteins: metabolism,Temperature,Thermodynamics},
month = may,
number = {19},
pages = {6083--93},
pmid = {18251533},
title = {{Simple continuous and discrete models for simulating replica exchange simulations of protein folding.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2978075\&tool=pmcentrez\&rendertype=abstract},
volume = {112},
year = {2008}
}
@article{Gallicchio2005,
abstract = {We analyzed the data from a replica exchange molecular dynamics simulation using the weighted histogram analysis method to combine data from all of the temperature replicas (T-WHAM) to obtain the room-temperature potential of mean force of the G-peptide (the C-terminal beta-hairpin of the B1 domain of protein G) in regions of conformational space not sampled at room temperature. We were able to determine the potential of mean force in the transition region between a minor alpha-helical population and the major beta-hairpin population and identify a possible transition path between them along which the peptide retains a significant amount of secondary structure. This observation provides new insights into a possible mechanism of formation of beta-sheet secondary structures in proteins. We developed a novel Bayesian statistical uncertainty estimation method for any quantity derived from WHAM and used it to validate the calculated potential of mean force. The feasibility of estimating regions of the potential of mean force with unfavorable free energy at room temperature by T-WHAM analysis of replica exchange simulations was further tested on a system that can be solved analytically and presented some of the same challenges found in more complex chemical systems.},
author = {Gallicchio, Emilio and Andrec, Michael and Felts, Anthony K and Levy, Ronald M},
doi = {10.1021/jp045294f},
file = {:Users/rnowling/Documents/Mendeley Desktop/Gallicchio et al/2005/Temperature weighted histogram analysis method, replica exchange, and transition paths/Gallicchio et al. - 2005 - Temperature weighted histogram analysis method, replica exchange, and transition paths.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
keywords = {Algorithms,Amino Acid Motifs,Bayes Theorem,Chemistry, Physical,Chemistry, Physical: methods,Computer Simulation,Likelihood Functions,Molecular Conformation,Monte Carlo Method,Peptides,Peptides: chemistry,Protein Conformation,Protein Structure, Secondary,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Temperature,Thermodynamics},
month = apr,
number = {14},
pages = {6722--31},
pmid = {16851756},
title = {{Temperature weighted histogram analysis method, replica exchange, and transition paths.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16851756},
volume = {109},
year = {2005}
}
@article{Faller2002,
author = {Faller, Roland and Yan, Qiliang and de Pablo, Juan J.},
doi = {10.1063/1.1456504},
file = {:Users/rnowling/Documents/Mendeley Desktop/Faller, Yan, de Pablo/2002/Multicanonical parallel tempering/Faller, Yan, de Pablo - 2002 - Multicanonical parallel tempering.pdf:pdf},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {13},
pages = {5419},
title = {{Multicanonical parallel tempering}},
url = {http://link.aip.org/link/JCPSA6/v116/i13/p5419/s1\&Agg=doi},
volume = {116},
year = {2002}
}
@article{Nymeyer2008,
author = {Nymeyer, Hugh},
doi = {10.1021/ct7003337},
file = {:Users/rnowling/Documents/Mendeley Desktop/Nymeyer/2008/How Efficient Is Replica Exchange Molecular Dynamics An Analytic Approach/Nymeyer - 2008 - How Efficient Is Replica Exchange Molecular Dynamics An Analytic Approach.pdf:pdf},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
month = apr,
number = {4},
pages = {626--636},
title = {{How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach}},
url = {http://pubs.acs.org/doi/abs/10.1021/ct7003337},
volume = {4},
year = {2008}
}
@article{Predescu2005,
abstract = {We introduce the concept of effective fraction, defined as the expected probability that a configuration from the lowest index replica successfully reaches the highest index replica during a replica exchange Monte Carlo simulation. We then argue that the effective fraction represents an adequate measure of the quality of the sampling technique, as far as swapping is concerned. Under the hypothesis that the correlation between successive exchanges is negligible, we propose a technique for the computation of the effective fraction, a technique that relies solely on the values of the acceptance probabilities obtained at the end of the simulation. The effective fraction is then utilized for the study of the efficiency of a popular swapping scheme in the context of parallel tempering in the canonical ensemble. For large dimensional oscillators, we show that the swapping probability that minimizes the computational effort is 38.74\%. By studying the parallel tempering swapping efficiency for a 13-atom Lennard-Jones cluster, we argue that the value of 38.74\% remains roughly the optimal probability for most systems with continuous distributions that are likely to be encountered in practice.},
author = {Predescu, Cristian and Predescu, Mihaela and Ciobanu, Cristian V},
doi = {10.1021/jp045073+},
file = {:Users/rnowling/Documents/Mendeley Desktop/Predescu, Predescu, Ciobanu/2005/On the efficiency of exchange in parallel tempering monte carlo simulations/Predescu, Predescu, Ciobanu - 2005 - On the efficiency of exchange in parallel tempering monte carlo simulations.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
month = mar,
number = {9},
pages = {4189--96},
pmid = {16851481},
title = {{On the efficiency of exchange in parallel tempering monte carlo simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16851481},
volume = {109},
year = {2005}
}
@article{Yang2007,
abstract = {We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G. The folding time prediction agrees quite well with experimental measurements. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties from all-atom "first-principles" models.},
author = {Yang, Sichun and Onuchic, Jos\'{e} N and Garc\'{\i}a, Angel E and Levine, Herbert},
doi = {10.1016/j.jmb.2007.07.010},
file = {:Users/rnowling/Documents/Mendeley Desktop/Yang et al/2007/Folding time predictions from all-atom replica exchange simulations/Yang et al. - 2007 - Folding time predictions from all-atom replica exchange simulations.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Computer Simulation,Diffusion,GTP-Binding Proteins,GTP-Binding Proteins: chemistry,GTP-Binding Proteins: metabolism,Hydrogen Bonding,Protein Folding,Protein Structure, Secondary,Temperature,Time Factors},
month = sep,
number = {3},
pages = {756--63},
pmid = {17681536},
title = {{Folding time predictions from all-atom replica exchange simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17681536},
volume = {372},
year = {2007}
}
@article{Jang2003,
author = {Jang, Soonmin and Shin, Seokmin and Pak, Youngshang},
doi = {10.1103/PhysRevLett.91.058305},
file = {:Users/rnowling/Documents/Mendeley Desktop/Jang, Shin, Pak/2003/Replica-Exchange Method Using the Generalized Effective Potential/Jang, Shin, Pak - 2003 - Replica-Exchange Method Using the Generalized Effective Potential.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = aug,
number = {5},
pages = {3--6},
title = {{Replica-Exchange Method Using the Generalized Effective Potential}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.91.058305},
volume = {91},
year = {2003}
}
@article{Rosta2009,
abstract = {We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water.},
author = {Rosta, Edina and Hummer, Gerhard},
doi = {10.1063/1.3249608},
file = {:Users/rnowling/Documents/Mendeley Desktop/Rosta, Hummer/2009/Error and efficiency of replica exchange molecular dynamics simulations/Rosta, Hummer - 2009 - Error and efficiency of replica exchange molecular dynamics simulations.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Kinetics,Molecular Dynamics Simulation,Oligopeptides,Oligopeptides: chemistry,Protein Denaturation,Protein Folding,Temperature,Thermodynamics,Time Factors},
month = oct,
number = {16},
pages = {165102},
pmid = {19894977},
title = {{Error and efficiency of replica exchange molecular dynamics simulations.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2780465\&tool=pmcentrez\&rendertype=abstract},
volume = {131},
year = {2009}
}
@article{Buchete2008a,
author = {Buchete, Nicolae-Viorel and Hummer, Gerhard},
doi = {10.1103/PhysRevE.77.030902},
file = {:Users/rnowling/Documents/Mendeley Desktop/Buchete, Hummer/2008/Peptide folding kinetics from replica exchange molecular dynamics/Buchete, Hummer - 2008 - Peptide folding kinetics from replica exchange molecular dynamics.pdf:pdf},
issn = {1539-3755},
journal = {Physical Review E},
month = mar,
number = {3},
pages = {1--4},
title = {{Peptide folding kinetics from replica exchange molecular dynamics}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.77.030902},
volume = {77},
year = {2008}
}
@article{Zhang2005,
abstract = {Replica exchange molecular dynamics (REMD) method is one of the generalized-ensemble algorithms which performs random walk in energy space and helps a system to escape from local energy traps. In this work, we studied the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics (MD) simulations and to enhance conformational sampling. Two sets of REMD simulations with different initial configurations, one from the fully extended and the other from fully helical conformations, were conducted on a fast-folding 21-amino-acid peptide with a continuum solvent model. Remarkably, the two REMD simulation sets started to converge even within 1.0 ns, despite their dramatically different starting conformations. In contrast, the conventional MD within the same time and with identical starting conformations did not show obvious signs of convergence. Excellent convergence between the REMD sets for T>300 K was observed after 14.0 ns REMD simulations as measured by the average helicity and free-energy profiles. We also conducted a set of 45 MD simulations at nine different temperatures with each trajectory simulated to 100.0 and 200.0 ns. An excellent agreement between the REMD and the extended MD simulation results was observed for T>300 K, showing that REMD can accurately reproduce long-time MD results with high efficiency. The autocorrelation times of the calculated helicity demonstrate that REMD can significantly enhance the sampling efficiency by 14.3+/-6.4, 35.1+/-0.2, and 71.5+/-20.4 times at, respectively, approximately 360, approximately 300, and approximately 275 K in comparison to the regular MD. Convergence was less satisfactory at low temperatures (T<300 K) and a slow oscillatory behavior suggests that longer simulation time was needed to reach equilibrium. Other technical issues, including choice of exchange frequency, were also examined.},
author = {Zhang, Wei and Wu, Chun and Duan, Yong},
doi = {10.1063/1.2056540},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zhang, Wu, Duan/2005/Convergence of replica exchange molecular dynamics/Zhang, Wu, Duan - 2005 - Convergence of replica exchange molecular dynamics.pdf:pdf},
issn = {0021-9606},
journal = {The Journal of chemical physics},
keywords = {Algorithms,Amino Acid Sequence,Computer Simulation,Models, Molecular,Molecular Sequence Data,Peptides,Peptides: chemistry,Protein Folding,Temperature},
month = oct,
number = {15},
pages = {154105},
pmid = {16252940},
title = {{Convergence of replica exchange molecular dynamics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16252940},
volume = {123},
year = {2005}
}
@article{Okabe2001,
author = {Okabe, Tsuneyasu and Kawata, Masaaki and Okamoto, Yuko and Mikami, Masuhiro},
doi = {10.1016/S0009-2614(01)00055-0},
file = {:Users/rnowling/Documents/Mendeley Desktop/Okabe et al/2001/Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble/Okabe et al. - 2001 - Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble.pdf:pdf},
issn = {00092614},
journal = {Chemical physics letters},
month = mar,
number = {5-6},
pages = {435--439},
publisher = {Elsevier},
title = {{Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009261401000550 http://www.sciencedirect.com/science/article/pii/S0009261401000550},
volume = {335},
year = {2001}
}
@article{Li2009,
author = {Li, Yaohang and Protopopescu, Vladimir a. and Arnold, Nikita and Zhang, Xinyu and Gorin, Andrey},
doi = {10.1016/j.amc.2009.02.023},
file = {:Users/rnowling/Documents/Mendeley Desktop/Li et al/2009/Hybrid parallel tempering and simulated annealing method/Li et al. - 2009 - Hybrid parallel tempering and simulated annealing method.pdf:pdf},
issn = {00963003},
journal = {Applied Mathematics and Computation},
keywords = {markov chain monte carlo},
month = jun,
number = {1},
pages = {216--228},
publisher = {Elsevier Inc.},
title = {{Hybrid parallel tempering and simulated annealing method}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0096300309001362},
volume = {212},
year = {2009}
}
@article{Mao1990,
author = {Mao, Boryeu and Friedman, Alan R.},
doi = {10.1016/S0006-3495(90)82424-3},
file = {:Users/rnowling/Documents/Mendeley Desktop/Mao, Friedman/1990/Molecular dynamics simulation by atomic mass weighting/Mao, Friedman - 1990 - Molecular dynamics simulation by atomic mass weighting.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
month = sep,
number = {3},
pages = {803--805},
publisher = {Elsevier},
title = {{Molecular dynamics simulation by atomic mass weighting}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349590824243},
volume = {58},
year = {1990}
}
@article{Schlick1997,
abstract = {Innovative algorithms have been developed during the past decade for simulating Newtonian physics for macromolecules. A major goal is alleviation of the severe requirement that the integration timestep be small enough to resolve the fastest components of the motion and thus guarantee numerical stability. This timestep problem is challenging if strictly faster methods with the same all-atom resolution at small timesteps are sought. Mathematical techniques that have worked well in other multiple-timescale contexts--where the fast motions are rapidly decaying or largely decoupled from others--have not been as successful for biomolecules, where vibrational coupling is strong. This review examines general issues that limit the timestep and describes available methods (constrained, reduced-variable, implicit, symplectic, multiple-timestep, and normal-mode-based schemes). A section compares results of selected integrators for a model dipeptide, assessing physical and numerical performance. Included is our dual timestep method LN, which relies on an approximate linearization of the equations of motion every delta t interval (5 fs or less), the solution of which is obtained by explicit integration at the inner timestep delta tau (e.g., 0.5 fs). LN is computationally competitive, providing 4-5 speedup factors, and results are in good agreement, in comparison to 0.5 fs trajectories. These collective algorithmic efforts help fill the gap between the time range that can be simulated and the timespans of major biological interest (milliseconds and longer). Still, only a hierarchy of models and methods, along with experimentational improvements, will ultimately give theoretical modeling the status of partner with experiment.},
author = {Schlick, T and Barth, E and Mandziuk, M},
doi = {10.1146/annurev.biophys.26.1.181},
file = {:Users/rnowling/Documents/Mendeley Desktop/Schlick, Barth, Mandziuk/1997/Biomolecular dynamics at long timesteps bridging the timescale gap between simulation and experimentation/Schlick, Barth, Mandziuk - 1997 - Biomolecular dynamics at long timesteps bridging the timescale gap between simulation and experimentation.pdf:pdf},
issn = {1056-8700},
journal = {Annual review of biophysics and biomolecular structure},
keywords = {Algorithms,Computer Simulation,Dipeptides,Dipeptides: chemistry,Models, Molecular,Molecular Structure,Protein Conformation,Proteins,Proteins: chemistry},
month = jan,
pages = {181--222},
pmid = {9241418},
title = {{Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9241418},
volume = {26},
year = {1997}
}
@article{Cooke2008,
abstract = {We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.},
annote = {Shows that REMD is not ergodic if replicas are not ergodic.  Shows that various isothermic methods are not ergodic -- Langevin remains "unknown" -- and presents a hybrid Monte Carlo (HMC) correction to fix non-ergodic methods.},
author = {Cooke, Ben and Schmidler, Scott C},
doi = {10.1063/1.2989802},
file = {:Users/rnowling/Documents/Mendeley Desktop/Cooke, Schmidler/2008/Preserving the Boltzmann ensemble in replica-exchange molecular dynamics/Cooke, Schmidler - 2008 - Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Alanine,Alanine: chemistry,Algorithms,Annotated,Dipeptides,Dipeptides: chemistry,Markov Chains,Models,Molecular,Monte Carlo Method,Protein Conformation,REMD,Sampling,Temperature,Thermodynamics},
mendeley-tags = {Annotated,REMD,Sampling},
month = oct,
number = {16},
pages = {164112},
pmid = {19045252},
title = {{Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19045252},
volume = {129},
year = {2008}
}
@article{Cooke2008,
abstract = {We describe a statistical approach to the validation and improvement of molecular dynamics simulations of macromolecules. We emphasize the use of molecular dynamics simulations to calculate thermodynamic quantities that may be compared to experimental measurements, and the use of a common set of energetic parameters across multiple distinct molecules. We briefly review relevant results from the theory of stochastic processes and discuss the monitoring of convergence to equilibrium, the obtaining of confidence intervals for summary statistics corresponding to measured quantities, and an approach to validation and improvement of simulations based on out-of-sample prediction. We apply these methods to replica exchange molecular dynamics simulations of a set of eight helical peptides under the AMBER potential using implicit solvent. We evaluate the ability of these simulations to quantitatively reproduce experimental helicity measurements obtained by circular dichroism. In addition, we introduce notions of statistical predictive estimation for force-field parameter refinement. We perform a sensitivity analysis to identify key parameters of the potential, and introduce Bayesian updating of these parameters. We demonstrate the effect of parameter updating applied to the internal dielectric constant parameter on the out-of-sample prediction accuracy as measured by cross-validation.},
author = {Cooke, Ben and Schmidler, Scott C},
doi = {10.1529/biophysj.108.131623},
file = {:Users/rnowling/Documents/Mendeley Desktop/Cooke, Schmidler/2008/Statistical prediction and molecular dynamics simulation/Cooke, Schmidler - 2008 - Statistical prediction and molecular dynamics simulation.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Computer Simulation,Models, Chemical,Models, Molecular,Models, Statistical,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Proteins: ultrastructure},
month = nov,
number = {10},
pages = {4497--511},
pmid = {18676654},
publisher = {Elsevier},
title = {{Statistical prediction and molecular dynamics simulation.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2576400\&tool=pmcentrez\&rendertype=abstract},
volume = {95},
year = {2008}
}
@article{Buchete2008,
abstract = {We construct coarse master equations for peptide folding dynamics from atomistic molecular dynamics simulations. A maximum-likelihood propagator-based method allows us to extract accurate rates for the transitions between the different conformational states of the small helix-forming peptide Ala5. Assigning the conformational states by using transition paths instead of instantaneous molecular coordinates suppresses the effects of fast non-Markovian dynamics. The resulting master equations are validated by comparing their analytical correlation functions with those obtained directly from the molecular dynamics simulations. We find that the master equations properly capture the character and relaxation times of the entire spectrum of conformational relaxation processes. By using the eigenvectors of the transition rate matrix, we are able to systematically coarse-grain the system. We find that a two-state description, with a folded and an unfolded state, roughly captures the slow conformational dynamics. A four-state model, with two folded and two unfolded states, accurately recovers the three slowest relaxation process with time scales between 1.5 and 7 ns. The master equation models not only give access to the slow conformational dynamics but also shed light on the molecular mechanisms of the helix-coil transition.},
author = {Buchete, Nicolae-Viorel and Hummer, Gerhard},
doi = {10.1021/jp0761665},
file = {:Users/rnowling/Documents/Mendeley Desktop/Buchete, Hummer/2008/Coarse master equations for peptide folding dynamics/Buchete, Hummer - 2008 - Coarse master equations for peptide folding dynamics.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
keywords = {Computer Simulation,Models, Molecular,Peptides,Peptides: chemistry,Protein Folding,Protein Structure, Tertiary,Temperature,Time Factors},
month = may,
number = {19},
pages = {6057--69},
pmid = {18232681},
title = {{Coarse master equations for peptide folding dynamics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18232681},
volume = {112},
year = {2008}
}
@article{Vyas2009,
abstract = {One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.},
annote = {Describes a basic formal grammar for describing minimotifs and their interactions with other molecules.},
author = {Vyas, Jay and Nowling, Ronald J and Maciejewski, Mark W and Rajasekaran, Sanguthevar and Gryk, Michael R and Schiller, Martin R},
doi = {10.1186/1471-2164-10-360},
file = {:Users/rnowling/Documents/Mendeley Desktop/Vyas et al/2009/A proposed syntax for Minimotif Semantics, version 1/Vyas et al. - 2009 - A proposed syntax for Minimotif Semantics, version 1.pdf:pdf},
issn = {1471-2164},
journal = {BMC genomics},
keywords = {Amino Acid Motifs,Annotated,Computational Biology,Computational Biology: methods,Database Management Systems,Databases,Protein,Protein Interaction Domains and Motifs,Semantics},
mendeley-tags = {Annotated},
month = jan,
pages = {360},
pmid = {19656396},
title = {{A proposed syntax for Minimotif Semantics, version 1.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2733157\&tool=pmcentrez\&rendertype=abstract},
volume = {10},
year = {2009}
}
@article{Vyas2010,
abstract = {Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.},
annote = {Describes system for managing minimotif database and facilitating faster annotation of papers through basic text mining to identify papers of interest and integration with Pubmed.},
author = {Vyas, Jay and Nowling, Ronald J and Meusburger, Thomas and Sargeant, David and Kadaveru, Krishna and Gryk, Michael R and Kundeti, Vamsi and Rajasekaran, Sanguthevar and Schiller, Martin R},
doi = {10.1186/1471-2105-11-328},
file = {:Users/rnowling/Documents/Mendeley Desktop/Vyas et al/2010/MimoSA a system for minimotif annotation/Vyas et al. - 2010 - MimoSA a system for minimotif annotation.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Algorithms,Amino Acid Motifs,Animals,Annotated,Artificial Intelligence,Data Mining,Data Mining: methods,Databases,Humans,Protein,Protein Binding,Proteins,Proteins: chemistry,Proteins: metabolism,Sequence Analysis},
mendeley-tags = {Annotated},
month = jan,
pages = {328},
pmid = {20565705},
title = {{MimoSA: a system for minimotif annotation.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2905367\&tool=pmcentrez\&rendertype=abstract},
volume = {11},
year = {2010}
}
@book{Casella2002,
author = {Casella, George and Berger, Roger L.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Casella, Berger/2002/Statistical Inference, 2e/Casella, Berger - 2002 - Statistical Inference, 2e.pdf:pdf},
title = {{Statistical Inference, 2e}},
year = {2002}
}
@article{Hu2008,
abstract = {O(6)-alkylguanine-DNA alkyltransferase (AGT) repairs damage to the human genome by flipping guanine and thymine bases into its active site for irreversible transfer of alkyl lesions to Cys-145, but how the protein identifies its targets has remained unknown. Understanding molecular recognition in this system, which can serve as a paradigm for the many nucleotide-flipping proteins that regulate genes and repair DNA in all kingdoms of life, is particularly important given that inhibitors are in clinical trials as anticancer therapeutics. Computational approaches introduced recently for harvesting and statistically characterizing trajectories of molecularly rare events now enable us to elucidate a pathway for nucleotide flipping by AGT and the forces that promote it. In contrast to previously proposed flipping mechanisms, we observe a two-step process that promotes a kinetic, rather than a thermodynamic, gate-keeping strategy for lesion discrimination. Connection is made to recent single-molecule studies of DNA-repair proteins sliding on DNA to understand how they sense subtle chemical differences between bases efficiently.},
author = {Hu, Jie and Ma, Ao and Dinner, Aaron R},
doi = {10.1073/pnas.0708058105},
file = {:Users/rnowling/Documents/Mendeley Desktop/Hu, Ma, Dinner/2008/A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT/Hu, Ma, Dinner - 2008 - A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Binding Sites,Computer Simulation,DNA,DNA Damage,DNA: chemistry,Guanine,Guanine: analogs \& derivatives,Guanine: metabolism,Humans,Kinetics,Nucleic Acid Conformation,Nucleotides,Nucleotides: metabolism,O(6)-Methylguanine-DNA Methyltransferase,O(6)-Methylguanine-DNA Methyltransferase: chemistr,O(6)-Methylguanine-DNA Methyltransferase: metaboli,Protein Structure, Secondary,Static Electricity,Thermodynamics,Tyrosine,Tyrosine: metabolism},
month = mar,
number = {12},
pages = {4615--20},
pmid = {18353991},
title = {{A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2290773\&tool=pmcentrez\&rendertype=abstract},
volume = {105},
year = {2008}
}
@article{Ma2005,
abstract = {To interpret simulations of a complex system to determine the physical mechanism of a dynamical process, it is necessary to identify the small number of coordinates that distinguish the stable states from the transition states. We develop an automatic method for identifying these degrees of freedom from a database of candidate physical variables. In the method neural networks are used to determine the functional dependence of the probability of committing to a stable state (committor) on a set of coordinates, and a genetic algorithm selects the combination of inputs that yields the best fit. The method enables us to obtain the first set of coordinates that is demonstrably sufficient to specify the transition state of the C(7eq)--> alpha(R) isomerization of the alanine dipeptide in the presence of explicit water molecules. It is revealed that the solute-solvent coupling can be described by a solvent-derived electrostatic torque around one of the main-chain bonds, and the collective, long-ranged nature of this interaction accounts for previous failures to characterize this reaction.},
author = {Ma, Ao and Dinner, Aaron R},
doi = {10.1021/jp045546c},
file = {:Users/rnowling/Documents/Mendeley Desktop/Ma, Dinner/2005/Automatic method for identifying reaction coordinates in complex systems/Ma, Dinner - 2005 - Automatic method for identifying reaction coordinates in complex systems.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
keywords = {Alanine,Alanine: chemistry,Automation,Carbon,Carbon: chemistry,Computer Simulation,Dipeptides,Dipeptides: chemistry,Models, Chemical,Models, Genetic,Models, Molecular,Models, Theoretical,Molecular Conformation,Neural Networks (Computer),Solvents,Solvents: chemistry,Static Electricity,Systems Biology,Thermodynamics},
month = apr,
number = {14},
pages = {6769--79},
pmid = {16851762},
title = {{Automatic method for identifying reaction coordinates in complex systems.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16851762},
volume = {109},
year = {2005}
}
@article{Qi2010,
abstract = {Simulations are important for understanding complex reactions, but their interpretation is challenging owing to the large number of degrees of freedom typically involved. To address this issue, various means for relating the dynamics of a stochastic system to its structural and energetic features have been introduced. Here, we show how two leading approaches can be combined to advantage. We use the network of transitions observed in a reversible folding/unfolding simulation of a 20-residue three-stranded antiparallel beta-sheet peptide (beta3s) to estimate the probabilities of committing to stable states (the native state and major nonnative states), and these then serve as the basis for an efficient statistical procedure for identifying physical variables that describe the dynamics. We find that a single coordinate that jointly characterizes the formation of the two native turns of beta3s can adequately describe the overall folding process, despite its complex nature. Additional features associated with major pathways leading from individual nonnative states are resolved; indeed, a key result is an improved understanding of the unfolded state. Connections to other methods for analyzing complex reactions are discussed.},
author = {Qi, Bo and Muff, Stefanie and Caflisch, Amedeo and Dinner, Aaron R},
doi = {10.1021/jp101476g},
file = {:Users/rnowling/Documents/Mendeley Desktop/Qi et al/2010/Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein/Qi et al. - 2010 - Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein.pdf:pdf},
issn = {1520-5207},
journal = {The journal of physical chemistry. B},
keywords = {Hydrogen Bonding,Peptides,Peptides: chemistry,Protein Denaturation,Protein Folding,Protein Structure, Secondary},
month = may,
number = {20},
pages = {6979--89},
pmid = {20438066},
title = {{Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20438066},
volume = {114},
year = {2010}
}
@article{Bahar2010,
annote = {Nice review of NMA, elastic network models (ENM), several block methods (RTB, BNM), and applications to studying membrane, transporter, and receptor proteins.  Includes interesting comparisons between coarse-grained NMA and full atomistic NMA.},
author = {Bahar, Ivet and Lezon, Timothy R and Bakan, Ahmet and Shrivastava, Indira H},
doi = {10.1021/cr900095e},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bahar et al/2010/Normal mode analysis of biomolecular structures functional mechanisms of membrane proteins/Bahar et al. - 2010 - Normal mode analysis of biomolecular structures functional mechanisms of membrane proteins.pdf:pdf},
issn = {1520-6890},
journal = {Chemical reviews},
keywords = {Allosteric Regulation,Animals,Annotated,Diagonalization,Humans,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: metabolism,Models,Molecular,NMA,Protein Conformation,Protein Multimerization},
mendeley-tags = {Annotated,Diagonalization,NMA},
month = mar,
number = {3},
pages = {1463--97},
pmid = {19785456},
title = {{Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2836427\&tool=pmcentrez\&rendertype=abstract},
volume = {110},
year = {2010}
}
@article{Lin2010,
abstract = {When only equilibrium thermodynamics or averages of position-dependent functions in classical molecular dynamics calculations are sought, the choice of the atomic masses in the Hamiltonian becomes irrelevant. Consequently, the masses can be used as free parameters to help improve conformational sampling efficiency in the spirit of Bennett's mass-tensor dynamics (Bennett, C. H. J. Comput. Phys. 1975, 19, 267.). Here we report on the effect of reducing side-chain and solvent masses on the folding behavior of a 9-residue hairpin-forming peptide in solution. A physical motivation for reducing the solvent mass is an effective reduction in solvent viscosity. Side-chain mass scaling is motivated by the idea of solvent potentials of mean force which are employed in select coarse-grained protein models. In the limit of very large mass differences, the mass reduction effectively creates an adiabatic decoupling between solvent, side-chain, and backbone motions, so that both the backbone and side chains move on the instantaneous solvent potential of mean force (PMF) surface, and the backbone additionally moves on the side-chain PMF. Because of the arbitrariness in the choice of masses, this limit only needs to be reached approximately in practice. In particular, we show that a 10-fold reduction in solvent masses and a side-chain mass scale that is intermediate between the scaled solvent and the backbone lead to a quantitative enhancement in conformational sampling.},
annote = {Describes simulations with reduced mass water (0.1) and side chains (0.4, 0.6, 0.8).  Mass irrelevant when computing averages of observables that depend only on position.  Improves sampling -- 0.6 and 0.8 reach states, <1 C-alpha RMSD that control, reduced mass water only, and 0.4 do not.   Choice of reduced mass matters -- mass disparity between solvent and side chains should be large enough to approximate adiabatic decoupling.  Ideas: too few simulations for each method, simulations too short, non-ergodic thermostatting methods (apply HMC corrections, other thermostatting methods?), and can we recover full dynamics with NML using reduced masses for Hessians and propagate with full masses?},
author = {Lin, I-Chun and Tuckerman, Mark E},
doi = {10.1021/jp109865y},
file = {:Users/rnowling/Documents/Mendeley Desktop/Lin, Tuckerman/2010/Enhanced conformational sampling of peptides via reduced side-chain and solvent masses/Lin, Tuckerman - 2010 - Enhanced conformational sampling of peptides via reduced side-chain and solvent masses.pdf:pdf},
issn = {1520-5207},
journal = {The journal of physical chemistry. B},
keywords = {Annotated,Lightwater,Models,Molecular,Molecular Dynamics Simulation,Molecular Weight,Peptides,Peptides: chemistry,Protein Conformation,Sampling,Solvents,Solvents: chemistry,Thermodynamics,Viscosity},
mendeley-tags = {Annotated,Lightwater,Sampling},
month = dec,
number = {48},
pages = {15935--40},
pmid = {21077595},
title = {{Enhanced conformational sampling of peptides via reduced side-chain and solvent masses.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21077595},
volume = {114},
year = {2010}
}
@article{Minary2004,
author = {Minary, P. and Tuckerman, M. and Martyna, G.},
doi = {10.1103/PhysRevLett.93.150201},
file = {:Users/rnowling/Documents/Mendeley Desktop/Minary, Tuckerman, Martyna/2004/Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems/Minary, Tuckerman, Martyna - 2004 - Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = oct,
number = {15},
pages = {1--4},
title = {{Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.93.150201},
volume = {93},
year = {2004}
}
@article{Barth1998,
author = {Barth, Eric and Schlick, Tamar},
doi = {10.1063/1.476736},
file = {:Users/rnowling/Documents/Mendeley Desktop/Barth, Schlick/1998/Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN/Barth, Schlick - 1998 - Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN.pdf:pdf},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {5},
pages = {1617},
title = {{Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN}},
url = {http://link.aip.org/link/JCPSA6/v109/i5/p1617/s1\&Agg=doi},
volume = {109},
year = {1998}
}
@article{Barth1998a,
author = {Barth, Eric and Schlick, Tamar},
doi = {10.1063/1.476737},
file = {:Users/rnowling/Documents/Mendeley Desktop/Barth, Schlick/1998/Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics/Barth, Schlick - 1998 - Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics.pdf:pdf},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {5},
pages = {1633},
title = {{Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics}},
url = {http://link.aip.org/link/JCPSA6/v109/i5/p1633/s1\&Agg=doi},
volume = {109},
year = {1998}
}
@inproceedings{Shaw2009,
author = {Shaw, D.E. and Dror, R.O. and Salmon, J.K. and Grossman, JP and Mackenzie, K.M. and Bank, J.A. and Young, Cliff and Deneroff, M.M. and Batson, Brannon and Bowers, K.J. and Others},
booktitle = {Proceedings of the ACM/IEEE Conference on Supercomputing (SC09)},
file = {:Users/rnowling/Documents/Mendeley Desktop/Shaw et al/2009/Millisecond-scale molecular dynamics simulations on Anton/Shaw et al. - 2009 - Millisecond-scale molecular dynamics simulations on Anton.pdf:pdf},
number = {c},
pages = {65},
publisher = {ACM},
title = {{Millisecond-scale molecular dynamics simulations on Anton}},
url = {http://portal.acm.org/citation.cfm?id=1654126},
year = {2009}
}
@article{Shaw2008,
author = {Shaw, D.E. and Deneroff, M.M. and Dror, R.O. and Kuskin, J.S. and Larson, R.H. and Salmon, J.K. and Young, Cliff and Batson, B. and Bowers, K.J. and Chao, J.C. and Others},
doi = {10.1145/1364782},
file = {:Users/rnowling/Documents/Mendeley Desktop/Shaw et al/2008/Anton, a special-purpose machine for molecular dynamics simulation/Shaw et al. - 2008 - Anton, a special-purpose machine for molecular dynamics simulation.pdf:pdf},
journal = {Communications of the ACM},
number = {2},
pages = {91--97},
publisher = {ACM},
title = {{Anton, a special-purpose machine for molecular dynamics simulation}},
url = {http://portal.acm.org/citation.cfm?id=1250664},
volume = {35},
year = {2008}
}
@article{Shaw2007,
author = {Shaw, David E. and Chao, Jack C. and Eastwood, Michael P. and Gagliardo, Joseph and Grossman, J. P. and Ho, C. Richard and Ierardi, Douglas J. and Kolossv\'{a}ry, Istv\'{a}n and Klepeis, John L. and Layman, Timothy and McLeavey, Christine and Deneroff, Martin M. and Moraes, Mark a. and Mueller, Rolf and Priest, Edward C. and Shan, Yibing and Spengler, Jochen and Theobald, Michael and Towles, Brian and Wang, Stanley C. and Dror, Ron O. and Kuskin, Jeffrey S. and Larson, Richard H. and Salmon, John K. and Young, Cliff and Batson, Brannon and Bowers, Kevin J.},
doi = {10.1145/1273440.1250664},
file = {:Users/rnowling/Documents/Mendeley Desktop/Shaw et al/2007/Anton, a special-purpose machine for molecular dynamics simulation/Shaw et al. - 2007 - Anton, a special-purpose machine for molecular dynamics simulation.pdf:pdf},
issn = {01635964},
journal = {ACM SIGARCH Computer Architecture News},
keywords = {bio-,computational biology,computational drug design,molecular dynamics,molecular system simulation,protein,protein folding,special-purpose machine,structure},
month = jun,
number = {2},
pages = {1},
title = {{Anton, a special-purpose machine for molecular dynamics simulation}},
url = {http://portal.acm.org/citation.cfm?doid=1273440.1250664},
volume = {35},
year = {2007}
}
@article{Ma2003,
author = {Ma, Qun and Izaguirre, J.A. and Skeel, R.D.},
doi = {10.1137/S1064827501399833},
file = {:Users/rnowling/Documents/Mendeley Desktop/Ma, Izaguirre, Skeel/2003/Verlet-Ir-RESPAImpulse is limited by nonlinear instabilities/Ma, Izaguirre, Skeel - 2003 - Verlet-Ir-RESPAImpulse is limited by nonlinear instabilities.pdf:pdf},
issn = {10648275},
journal = {SIAM Journal on Scientific Computing},
keywords = {34d04,65l05,70f04,70f08,ams subject classifications,impulse,kam theory,langevin stabilization,long molecular dynamics simulations,mollified impulse method,multiple time,nonlinear instability,pii,r-respa,s1064827501399833,stepping,verlet-i},
number = {6},
pages = {1951--1973},
publisher = {Citeseer},
title = {{Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities}},
url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.76.2183\&amp;rep=rep1\&amp;type=pdf},
volume = {24},
year = {2003}
}
@incollection{Izaguirre1998,
address = {Berlin},
author = {Izaguirre, Jes\'{u}s a. and Skeel, Robert D.},
booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas, Vol. 4 of Lecture Notes in Computational Science \& Engineering},
pages = {303--318},
publisher = {Springer-Verlag},
title = {{The Five Femtosecond Time Step Barrier}},
year = {1998}
}
@book{Schlick2006,
address = {New York, NY},
author = {Schlick, Tamar},
editor = {Marsden, JE and Wiggins, S and Sirovich, L and Antman, SS},
isbn = {0-387-95404-X},
publisher = {Springer Science+Business Media, LLC},
title = {{Molecular Modeling and Simulation: An Interdisciplinary Guide}},
year = {2006}
}
@article{Zhou2008,
abstract = {Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics.},
author = {Zhou, Lei and Siegelbaum, Steven a},
doi = {10.1529/biophysj.107.115956},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zhou, Siegelbaum/2008/Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach/Zhou, Siegelbaum - 2008 - Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Ion Channels,Ion Channels: chemistry,Ion Channels: metabolism,Models, Chemical,Movement,Movement: drug effects,Nucleotides, Cyclic,Nucleotides, Cyclic: chemistry,Nucleotides, Cyclic: metabolism,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Proteins: metabolism,Surface Properties,Temperature,Vibration,Water,Water: pharmacology},
month = may,
number = {9},
pages = {3461--74},
pmid = {18212016},
title = {{Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18212016},
volume = {94},
year = {2008}
}
@article{Skeel1997,
author = {Skeel, Robert D. and Zhang, Guihua and Schlick, Tamar},
doi = {10.1137/S1064827595282350},
file = {:Users/rnowling/Documents/Mendeley Desktop/Skeel, Zhang, Schlick/1997/A Family of Symplectic Integrators Stability, Accuracy, and Molecular Dynamics Applications/Skeel, Zhang, Schlick - 1997 - A Family of Symplectic Integrators Stability, Accuracy, and Molecular Dynamics Applications.pdf:pdf},
issn = {10648275},
journal = {SIAM Journal on Scientific Computing},
keywords = {65l20,ams subject classification,cowell,implicit midpoint,leapfrog,method of modified equations,molecular dynamics,numerov,ormer,plectic integrator,st,sym-,trapezoid,verlet},
number = {1},
pages = {203},
title = {{A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications}},
url = {http://link.aip.org/link/SJOCE3/v18/i1/p203/s1\&Agg=doi},
volume = {18},
year = {1997}
}
@article{Toroczkai2008,
author = {Toroczkai, Zolt\'{a}n and Kozma, Bal\'{a}zs and Bassler, Kevin E and Hengartner, NW and Korniss, G},
doi = {10.1088/1751-8113/41/15/155103},
file = {:Users/rnowling/Documents/Mendeley Desktop/Toroczkai et al/2008/Gradient networks/Toroczkai et al. - 2008 - Gradient networks.pdf:pdf},
issn = {1751-8113},
journal = {Journal of Physics A: Mathematical and Theoretical},
month = apr,
number = {15},
pages = {155103},
title = {{Gradient networks}},
url = {http://arxiv.org/abs/cond-mat/0408262},
volume = {41},
year = {2008}
}
@article{Durand2000,
author = {Durand, Philippe and {Xavier Gade´a}, Florent and Paidarov\'{a}, Ivana},
doi = {10.1039/b000001i},
file = {:Users/rnowling/Documents/Mendeley Desktop/Durand, Xavier Gade´a, Paidarov\'{a}/2000/Computational determination of wave operators from large Hamiltonian matrices/Durand, Xavier Gade´a, Paidarov\'{a} - 2000 - Computational determination of wave operators from large Hamiltonian matrices.pdf:pdf},
issn = {14639076},
journal = {Physical Chemistry Chemical Physics},
number = {13},
pages = {2829--2836},
title = {{Computational determination of wave operators from large Hamiltonian matrices}},
url = {http://xlink.rsc.org/?DOI=b000001i},
volume = {2},
year = {2000}
}
@article{Hubbard2002,
abstract = {The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.},
author = {Hubbard, T and Barker, D and Birney, E and Cameron, G and Chen, Y and Clark, L and Cox, T and Cuff, J and Curwen, V and Down, T and Durbin, R and Eyras, E and Gilbert, J and Hammond, M and Huminiecki, L and Kasprzyk, a and Lehvaslaiho, H and Lijnzaad, P and Melsopp, C and Mongin, E and Pettett, R and Pocock, M and Potter, S and Rust, a and Schmidt, E and Searle, S and Slater, G and Smith, J and Spooner, W and Stabenau, a and Stalker, J and Stupka, E and Ureta-Vidal, a and Vastrik, I and Clamp, M},
file = {:Users/rnowling/Documents/Mendeley Desktop/Hubbard et al/2002/The Ensembl genome database project/Hubbard et al. - 2002 - The Ensembl genome database project.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Computational Biology,Database Management Systems,Databases, Genetic,Genome, Human,Humans,Information Storage and Retrieval,Internet,Sequence Analysis, DNA,Systems Integration},
month = jan,
number = {1},
pages = {38--41},
pmid = {11752248},
title = {{The Ensembl genome database project.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=99161\&tool=pmcentrez\&rendertype=abstract},
volume = {30},
year = {2002}
}
@article{Zhang2006,
abstract = {G protein-coupled receptors (GPCRs), encoded by about 5\% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha) root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. All predicted GPCR models are freely available for noncommercial users on our Web site (http://www.bioinformatics.buffalo.edu/GPCR).},
author = {Zhang, Yang and Devries, Mark E and Skolnick, Jeffrey},
doi = {10.1371/journal.pcbi.0020013},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zhang, Devries, Skolnick/2006/Structure modeling of all identified G protein-coupled receptors in the human genome/Zhang, Devries, Skolnick - 2006 - Structure modeling of all identified G protein-coupled receptors in the human genome.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
keywords = {Algorithms,Animals,Cattle,Cluster Analysis,Computational Biology,Computational Biology: methods,Databases, Protein,Genome, Human,Humans,Internet,Models, Molecular,Molecular Conformation,Protein Conformation,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: chemistry,Software},
month = feb,
number = {2},
pages = {e13},
pmid = {16485037},
title = {{Structure modeling of all identified G protein-coupled receptors in the human genome.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1364505\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2006}
}
@article{Zhang2009,
abstract = {Computationally predicted three-dimensional structure of protein molecules has demonstrated the usefulness in many areas of biomedicine, ranging from approximate family assignments to precise drug screening. For nearly 40 years, however, the accuracy of the predicted models has been dictated by the availability of close structural templates. Progress has recently been achieved in refining low-resolution models closer to the native ones; this has been made possible by combining knowledge-based information from multiple sources of structural templates as well as by improving the energy funnel of physics-based force fields. Unfortunately, there has been no essential progress in the development of techniques for detecting remotely homologous templates and for predicting novel protein structures.},
author = {Zhang, Yang},
doi = {10.1016/j.sbi.2009.02.005},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zhang/2009/Protein structure prediction when is it useful/Zhang - 2009 - Protein structure prediction when is it useful.pdf:pdf},
issn = {1879-033X},
journal = {Current opinion in structural biology},
keywords = {Algorithms,Computational Biology,Computational Biology: methods,Computer Simulation,Databases, Protein,Humans,Models, Molecular,Protein Conformation,Proteins,Proteins: chemistry,Structure-Activity Relationship},
month = apr,
number = {2},
pages = {145--55},
pmid = {19327982},
title = {{Protein structure prediction: when is it useful?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19327982},
volume = {19},
year = {2009}
}
@article{Nene2007,
abstract = {We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50\% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.},
author = {Nene, Vishvanath and Wortman, Jennifer R and Lawson, Daniel and Haas, Brian and Kodira, Chinnappa and Tu, Zhijian Jake and Loftus, Brendan and Xi, Zhiyong and Megy, Karyn and Grabherr, Manfred and Ren, Quinghu and Zdobnov, Evgeny M and Lobo, Neil F and Campbell, Kathryn S and Brown, Susan E and Bonaldo, Maria F and Zhu, Jingsong and Sinkins, Steven P and Hogenkamp, David G and Amedeo, Paolo and Arensburger, Peter and Atkinson, Peter W and Bidwell, Shelby and Biedler, Jim and Birney, Ewan and Bruggner, Robert V and Costas, Javier and Coy, Monique R and Crabtree, Jonathan and Crawford, Matt and Debruyn, Becky and Decaprio, David and Eiglmeier, Karin and Eisenstadt, Eric and El-Dorry, Hamza and Gelbart, William M and Gomes, Suely L and Hammond, Martin and Hannick, Linda I and Hogan, James R and Holmes, Michael H and Jaffe, David and Johnston, J Spencer and Kennedy, Ryan C and Koo, Hean and Kravitz, Saul and Kriventseva, Evgenia V and Kulp, David and Labutti, Kurt and Lee, Eduardo and Li, Song and Lovin, Diane D and Mao, Chunhong and Mauceli, Evan and Menck, Carlos F M and Miller, Jason R and Montgomery, Philip and Mori, Akio and Nascimento, Ana L and Naveira, Horacio F and Nusbaum, Chad and O'leary, Sin\'{e}ad and Orvis, Joshua and Pertea, Mihaela and Quesneville, Hadi and Reidenbach, Kyanne R and Rogers, Yu-Hui and Roth, Charles W and Schneider, Jennifer R and Schatz, Michael and Shumway, Martin and Stanke, Mario and Stinson, Eric O and Tubio, Jose M C and Vanzee, Janice P and Verjovski-Almeida, Sergio and Werner, Doreen and White, Owen and Wyder, Stefan and Zeng, Qiandong and Zhao, Qi and Zhao, Yongmei and Hill, Catherine a and Raikhel, Alexander S and Soares, Marcelo B and Knudson, Dennis L and Lee, Norman H and Galagan, James and Salzberg, Steven L and Paulsen, Ian T and Dimopoulos, George and Collins, Frank H and Birren, Bruce and Fraser-Liggett, Claire M and Severson, David W},
doi = {10.1126/science.1138878},
file = {:Users/rnowling/Documents/Mendeley Desktop/Nene et al/2007/Genome sequence of Aedes aegypti, a major arbovirus vector/Nene et al. - 2007 - Genome sequence of Aedes aegypti, a major arbovirus vector.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Aedes,Aedes: genetics,Aedes: metabolism,Animals,Anopheles gambiae,Anopheles gambiae: genetics,Anopheles gambiae: metabolism,Arboviruses,Base Sequence,DNA Transposable Elements,Dengue,Dengue: prevention \& control,Dengue: transmission,Drosophila melanogaster,Drosophila melanogaster: genetics,Female,Genes, Insect,Genome, Insect,Humans,Insect Proteins,Insect Proteins: genetics,Insect Vectors,Insect Vectors: genetics,Insect Vectors: metabolism,Male,Membrane Transport Proteins,Membrane Transport Proteins: genetics,Molecular Sequence Data,Multigene Family,Protein Structure, Tertiary,Protein Structure, Tertiary: genetics,Sequence Analysis, DNA,Sex Characteristics,Sex Determination Processes,Species Specificity,Synteny,Transcription, Genetic,Yellow Fever,Yellow Fever: prevention \& control,Yellow Fever: transmission},
month = jun,
number = {5832},
pages = {1718--23},
pmid = {17510324},
title = {{Genome sequence of Aedes aegypti, a major arbovirus vector.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2868357\&tool=pmcentrez\&rendertype=abstract},
volume = {316},
year = {2007}
}
@article{Holt2002,
abstract = {Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91\% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.},
author = {Holt, Robert A and Subramanian, G Mani and Halpern, Aaron and Sutton, Granger G and Charlab, Rosane and Nusskern, Deborah R and Wincker, Patrick and Clark, Andrew G and Ribeiro, Jos\'{e} M C and Wides, Ron and Salzberg, Steven L and Loftus, Brendan and Yandell, Mark and Majoros, William H and Rusch, Douglas B and Lai, Zhongwu and Kraft, Cheryl L and Abril, Josep F and Anthouard, Veronique and Arensburger, Peter and Atkinson, Peter W and Baden, Holly and de Berardinis, Veronique and Baldwin, Danita and Benes, Vladimir and Biedler, Jim and Blass, Claudia and Bolanos, Randall and Boscus, Didier and Barnstead, Mary and Cai, Shuang and Center, Angela and Chaturverdi, Kabir and Christophides, George K and Chrystal, Mathew a and Clamp, Michele and Cravchik, Anibal and Curwen, Val and Dana, Ali and Delcher, Art and Dew, Ian and Evans, Cheryl a and Flanigan, Michael and Grundschober-Freimoser, Anne and Friedli, Lisa and Gu, Zhiping and Guan, Ping and Guigo, Roderic and Hillenmeyer, Maureen E and Hladun, Susanne L and Hogan, James R and Hong, Young S and Hoover, Jeffrey and Jaillon, Olivier and Ke, Zhaoxi and Kodira, Chinnappa and Kokoza, Elena and Koutsos, Anastasios and Letunic, Ivica and Levitsky, Alex and Liang, Yong and Lin, Jhy-Jhu and Lobo, Neil F and Lopez, John R and Malek, Joel a and McIntosh, Tina C and Meister, Stephan and Miller, Jason and Mobarry, Clark and Mongin, Emmanuel and Murphy, Sean D and O'Brochta, David a and Pfannkoch, Cynthia and Qi, Rong and Regier, Megan a and Remington, Karin and Shao, Hongguang and Sharakhova, Maria V and Sitter, Cynthia D and Shetty, Jyoti and Smith, Thomas J and Strong, Renee and Sun, Jingtao and Thomasova, Dana and Ton, Lucas Q and Topalis, Pantelis and Tu, Zhijian and Unger, Maria F and Walenz, Brian and Wang, Aihui and Wang, Jian and Wang, Mei and Wang, Xuelan and Woodford, Kerry J and Wortman, Jennifer R and Wu, Martin and Yao, Alison and Zdobnov, Evgeny M and Zhang, Hongyu and Zhao, Qi and Zhao, Shaying and Zhu, Shiaoping C and Zhimulev, Igor and Coluzzi, Mario and della Torre, Alessandra and Roth, Charles W and Louis, Christos and Kalush, Francis and Mural, Richard J and Myers, Eugene W and Adams, Mark D and Smith, Hamilton O and Broder, Samuel and Gardner, Malcolm J and Fraser, Claire M and Birney, Ewan and Bork, Peer and Brey, Paul T and Venter, J Craig and Weissenbach, Jean and Kafatos, Fotis C and Collins, Frank H and Hoffman, Stephen L},
doi = {10.1126/science.1076181},
file = {:Users/rnowling/Documents/Mendeley Desktop/Holt et al/2002/The genome sequence of the malaria mosquito Anopheles gambiae/Holt et al. - 2002 - The genome sequence of the malaria mosquito Anopheles gambiae.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Animals,Anopheles,Anopheles: classification,Anopheles: genetics,Anopheles: parasitology,Anopheles: physiology,Artificial,Bacterial,Blood,Chromosome Inversion,Chromosomes,Computational Biology,DNA,DNA Transposable Elements,Digestion,Drosophila melanogaster,Drosophila melanogaster: genetics,Enzymes,Enzymes: chemistry,Enzymes: genetics,Enzymes: metabolism,Evolution,Expressed Sequence Tags,Falciparum,Falciparum: transmission,Feeding Behavior,Gene Expression Regulation,Genes,Genetic Variation,Genome,Haplotypes,Humans,Insect,Insect Proteins,Insect Proteins: chemistry,Insect Proteins: genetics,Insect Proteins: physiology,Insect Vectors,Insect Vectors: genetics,Insect Vectors: parasitology,Insect Vectors: physiology,Malaria,Molecular Sequence Data,Mosquito Control,Physical Chromosome Mapping,Plasmodium falciparum,Plasmodium falciparum: growth \& development,Polymorphism,Proteome,Sequence Analysis,Single Nucleotide,Species Specificity,Transcription Factors,Transcription Factors: chemistry,Transcription Factors: genetics,Transcription Factors: physiology},
month = oct,
number = {5591},
pages = {129--49},
pmid = {12364791},
title = {{The genome sequence of the malaria mosquito Anopheles gambiae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12364791},
volume = {298},
year = {2002}
}
@article{Hill2002,
abstract = {We used bioinformatic approaches to identify a total of 276 G protein-coupled receptors (GPCRs) from the Anopheles gambiae genome. These include GPCRs that are likely to play roles in pathways affecting almost every aspect of the mosquito's life cycle. Seventy-nine candidate odorant receptors were characterized for tissue expression and, along with 76 putative gustatory receptors, for their molecular evolution relative to Drosophila melanogaster. Examples of lineage-specific gene expansions were observed as well as a single instance of unusually high sequence conservation.},
author = {Hill, Catherine A and Fox, A Nicole and Pitts, R Jason and Kent, Lauren B and Tan, Perciliz L and Chrystal, Mathew A and Cravchik, Anibal and Collins, Frank H and Robertson, Hugh M and Zwiebel, Laurence J},
doi = {10.1126/science.1076196},
file = {:Users/rnowling/Documents/Mendeley Desktop/Hill et al/2002/G protein-coupled receptors in Anopheles gambiae/Hill et al. - 2002 - G protein-coupled receptors in Anopheles gambiae.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Alternative Splicing,Amino Acid Sequence,Animals,Anopheles,Anopheles: chemistry,Anopheles: genetics,Anopheles: metabolism,Cell Surface,Cell Surface: chemistry,Cell Surface: genetics,Cell Surface: metabolism,Computational Biology,Conserved Sequence,Drosophila Proteins,Drosophila Proteins: chemistry,Drosophila Proteins: genetics,Drosophila Proteins: metabolism,Drosophila melanogaster,Drosophila melanogaster: chemistry,Drosophila melanogaster: genetics,Drosophila melanogaster: metabolism,Evolution,GTP-Binding Proteins,GTP-Binding Proteins: metabolism,Gene Amplification,Gene Expression,Genes,Genome,Insect,Insect Proteins,Insect Proteins: chemistry,Insect Proteins: genetics,Insect Proteins: metabolism,Molecular,Molecular Sequence Data,Multigene Family,Odorant,Odorant: chemistry,Odorant: genetics,Odorant: metabolism,Phylogeny,Receptors,Reverse Transcriptase Polymerase Chain Reaction,Signal Transduction},
month = oct,
number = {5591},
pages = {176--8},
pmid = {12364795},
title = {{G protein-coupled receptors in Anopheles gambiae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12364795},
volume = {298},
year = {2002}
}
@article{Lawson2007,
abstract = {VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.},
author = {Lawson, Daniel and Arensburger, Peter and Atkinson, Peter and Besansky, Nora J and Bruggner, Robert V and Butler, Ryan and Campbell, Kathryn S and Christophides, George K and Christley, Scott and Dialynas, Emmanuel and Emmert, David and Hammond, Martin and Hill, Catherine a and Kennedy, Ryan C and Lobo, Neil F and MacCallum, M Robert and Madey, Greg and Megy, Karine and Redmond, Seth and Russo, Susan and Severson, David W and Stinson, Eric O and Topalis, Pantelis and Zdobnov, Evgeny M and Birney, Ewan and Gelbart, William M and Kafatos, Fotis C and Louis, Christos and Collins, Frank H},
doi = {10.1093/nar/gkl960},
file = {:Users/rnowling/Documents/Mendeley Desktop/Lawson et al/2007/VectorBase a home for invertebrate vectors of human pathogens/Lawson et al. - 2007 - VectorBase a home for invertebrate vectors of human pathogens.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Aedes,Aedes: genetics,Animals,Anopheles gambiae,Anopheles gambiae: genetics,Base Sequence,Conserved Sequence,Databases, Genetic,Genome, Insect,Genomics,Humans,Insect Vectors,Insect Vectors: genetics,Internet,User-Computer Interface},
month = jan,
number = {Database issue},
pages = {D503--5},
pmid = {17145709},
title = {{VectorBase: a home for invertebrate vectors of human pathogens.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1751530\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{Lawson2009,
abstract = {VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data.},
author = {Lawson, Daniel and Arensburger, Peter and Atkinson, Peter and Besansky, Nora J and Bruggner, Robert V and Butler, Ryan and Campbell, Kathryn S and Christophides, George K and Christley, Scott and Dialynas, Emmanuel and Hammond, Martin and Hill, Catherine a and Konopinski, Nathan and Lobo, Neil F and MacCallum, Robert M and Madey, Greg and Megy, Karine and Meyer, Jason and Redmond, Seth and Severson, David W and Stinson, Eric O and Topalis, Pantelis and Birney, Ewan and Gelbart, William M and Kafatos, Fotis C and Louis, Christos and Collins, Frank H},
doi = {10.1093/nar/gkn857},
file = {:Users/rnowling/Documents/Mendeley Desktop/Lawson et al/2009/VectorBase a data resource for invertebrate vector genomics/Lawson et al. - 2009 - VectorBase a data resource for invertebrate vector genomics.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Aedes,Aedes: genetics,Animals,Anopheles gambiae,Anopheles gambiae: genetics,Arthropod Vectors,Arthropod Vectors: genetics,Culex,Culex: genetics,Culicidae,Culicidae: genetics,Culicidae: metabolism,Databases, Genetic,Gene Expression Profiling,Genome, Insect,Genomics,Ixodes,Ixodes: genetics,Pediculus,Pediculus: genetics,Vocabulary, Controlled},
month = jan,
number = {Database issue},
pages = {D583--7},
pmid = {19028744},
title = {{VectorBase: a data resource for invertebrate vector genomics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19028744},
volume = {37},
year = {2009}
}
@article{Tweedie2009,
abstract = {FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project--a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species.},
author = {Tweedie, Susan and Ashburner, Michael and Falls, Kathleen and Leyland, Paul and McQuilton, Peter and Marygold, Steven and Millburn, Gillian and Osumi-Sutherland, David and Schroeder, Andrew and Seal, Ruth and Zhang, Haiyan},
doi = {10.1093/nar/gkn788},
file = {:Users/rnowling/Documents/Mendeley Desktop/Tweedie et al/2009/FlyBase enhancing Drosophila Gene Ontology annotations/Tweedie et al. - 2009 - FlyBase enhancing Drosophila Gene Ontology annotations.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Animals,Databases, Genetic,Drosophila,Drosophila Proteins,Drosophila Proteins: genetics,Drosophila: genetics,Genes, Insect,Genome, Insect,Genomics,Vocabulary, Controlled},
month = jan,
number = {Database issue},
pages = {D555--9},
pmid = {18948289},
title = {{FlyBase: enhancing Drosophila Gene Ontology annotations.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2686450\&tool=pmcentrez\&rendertype=abstract},
volume = {37},
year = {2009}
}
@article{Gelbart1997,
author = {Gelbart, WM and Crosby, M. and Matthews, B. and Rindone, WP and Chillemi, J. and Twombly, S.R. and Emmert, D. and Ashburner, M. and Drysdale, RA and Whitfield, E. and Others},
doi = {10.1093/nar/25.1.63},
file = {:Users/rnowling/Documents/Mendeley Desktop/Gelbart et al/1997/FlyBase a Drosophila database. The FlyBase consortium/Gelbart et al. - 1997 - FlyBase a Drosophila database. The FlyBase consortium.pdf:pdf},
issn = {13624962},
journal = {Nucleic acids research},
month = jan,
number = {1},
pages = {63},
publisher = {Oxford University Press},
title = {{FlyBase: a Drosophila database. The FlyBase consortium.}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC146418/},
volume = {25},
year = {1997}
}
@article{Crosby2007,
abstract = {FlyBase (http://flybase.org/) is the primary database of genetic and genomic data for the insect family Drosophilidae. Historically, Drosophila melanogaster has been the most extensively studied species in this family, but recent determination of the genomic sequences of an additional 11 Drosophila species opens up new avenues of research for other Drosophila species. This extensive sequence resource, encompassing species with well-defined phylogenetic relationships, provides a model system for comparative genomic analyses. FlyBase has developed tools to facilitate access to and navigation through this invaluable new data collection.},
author = {Crosby, Madeline a and Goodman, Joshua L and Strelets, Victor B and Zhang, Peili and Gelbart, William M},
doi = {10.1093/nar/gkl827},
file = {:Users/rnowling/Documents/Mendeley Desktop/Crosby et al/2007/FlyBase genomes by the dozen/Crosby et al. - 2007 - FlyBase genomes by the dozen.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Animals,Databases, Genetic,Drosophila,Drosophila: classification,Drosophila: genetics,Drosophilidae,Drosophilidae: classification,Drosophilidae: genetics,Genome, Insect,Genomics,Internet,Phylogeny,Software,User-Computer Interface},
month = jan,
number = {Database issue},
pages = {D486--91},
pmid = {17099233},
title = {{FlyBase: genomes by the dozen.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1669768\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{Horn2003,
author = {Horn, F. and Bettler, E. and Oliveira, L. and Campagne, F. and Cohen, F.E. and Vriend, G.},
doi = {10.1093/nar/gkg103},
file = {:Users/rnowling/Documents/Mendeley Desktop/Horn et al/2003/GPCRDB information system for G protein-coupled receptors/Horn et al. - 2003 - GPCRDB information system for G protein-coupled receptors.pdf:pdf},
issn = {13624962},
journal = {Nucleic acids research},
month = jan,
number = {1},
pages = {294},
publisher = {Oxford Univ Press},
title = {{GPCRDB information system for G protein-coupled receptors}},
url = {http://nar.oxfordjournals.org/content/31/1/294.short},
volume = {31},
year = {2003}
}
@article{Finn2010,
abstract = {Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).},
author = {Finn, Robert D and Mistry, Jaina and Tate, John and Coggill, Penny and Heger, Andreas and Pollington, Joanne E and Gavin, O Luke and Gunasekaran, Prasad and Ceric, Goran and Forslund, Kristoffer and Holm, Liisa and Sonnhammer, Erik L L and Eddy, Sean R and Bateman, Alex},
doi = {10.1093/nar/gkp985},
file = {:Users/rnowling/Documents/Mendeley Desktop/Finn et al/2010/The Pfam protein families database/Finn et al. - 2010 - The Pfam protein families database.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Amino Acid Sequence,Animals,Computational Biology,Computational Biology: methods,Computational Biology: trends,Databases, Nucleic Acid,Databases, Protein,Genome, Archaeal,Genome, Fungal,Humans,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Molecular Sequence Data,Protein Structure, Tertiary,Sequence Alignment,Sequence Homology, Amino Acid,Software},
month = jan,
number = {Database issue},
pages = {D211--22},
pmid = {19920124},
title = {{The Pfam protein families database.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2808889\&tool=pmcentrez\&rendertype=abstract},
volume = {38},
year = {2010}
}
@article{Elofsson2007,
abstract = {Since high-resolution structural data are still scarce, different kinds of theoretical structure prediction algorithms are of major importance in membrane protein biochemistry. But how well do the current prediction methods perform? Which structural features can be predicted and which cannot? And what can we expect in the next few years?},
author = {Elofsson, Arne and von Heijne, Gunnar},
doi = {10.1146/annurev.biochem.76.052705.163539},
file = {:Users/rnowling/Documents/Mendeley Desktop/Elofsson, von Heijne/2007/Membrane protein structure prediction versus reality/Elofsson, von Heijne - 2007 - Membrane protein structure prediction versus reality.pdf:pdf},
issn = {0066-4154},
journal = {Annual review of biochemistry},
keywords = {Algorithms,Amino Acid Sequence,Computational Biology,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: classification,Membrane Proteins: genetics,Membrane Proteins: metabolism,Models, Molecular,Molecular Sequence Data,Protein Binding,Protein Conformation,Protein Folding},
month = jan,
pages = {125--40},
pmid = {17579561},
title = {{Membrane protein structure: prediction versus reality.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17579561},
volume = {76},
year = {2007}
}
@article{Punta2007,
abstract = {We survey computational approaches that tackle membrane protein structure and function prediction. While describing the main ideas that have led to the development of the most relevant and novel methods, we also discuss pitfalls, provide practical hints and highlight the challenges that remain. The methods covered include: sequence alignment, motif search, functional residue identification, transmembrane segment and protein topology predictions, homology and ab initio modeling. In general, predictions of functional and structural features of membrane proteins are improving, although progress is hampered by the limited amount of high-resolution experimental information available. While predictions of transmembrane segments and protein topology rank among the most accurate methods in computational biology, more attention and effort will be required in the future to ameliorate database search, homology and ab initio modeling.},
author = {Punta, Marco and Forrest, Lucy R and Bigelow, Henry and Kernytsky, Andrew and Liu, Jinfeng and Rost, Burkhard},
doi = {10.1016/j.ymeth.2006.07.026},
file = {:Users/rnowling/Documents/Mendeley Desktop/Punta et al/2007/Membrane protein prediction methods/Punta et al. - 2007 - Membrane protein prediction methods.pdf:pdf},
issn = {1046-2023},
journal = {Methods (San Diego, Calif.)},
keywords = {Biochemistry,Biochemistry: methods,Databases, Factual,Genomics,Membrane Proteins,Membrane Proteins: chemistry,Membrane Proteins: genetics,Models, Chemical,Predictive Value of Tests,Protein Conformation,Structure-Activity Relationship},
month = apr,
number = {4},
pages = {460--74},
pmid = {17367718},
title = {{Membrane protein prediction methods.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17367718},
volume = {41},
year = {2007}
}
@article{Davies2007,
abstract = {The G-protein coupled receptor (GPCR) superfamily fulfils various metabolic functions and interacts with a diverse range of ligands. There is a lack of sequence similarity between the six classes that comprise the GPCR superfamily. Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of their amino acid sequences. This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area.},
author = {Davies, Matthew N and Gloriam, David E and Secker, Andrew and Freitas, Alex a and Mendao, Miguel and Timmis, Jon and Flower, Darren R},
doi = {10.1002/pmic.200700093},
file = {:Users/rnowling/Documents/Mendeley Desktop/Davies et al/2007/Proteomic applications of automated GPCR classification/Davies et al. - 2007 - Proteomic applications of automated GPCR classification.pdf:pdf},
issn = {1615-9853},
journal = {Proteomics},
keywords = {Automation,Markov Chains,Proteomics,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: chemistry,Receptors, G-Protein-Coupled: classification},
month = aug,
number = {16},
pages = {2800--14},
pmid = {17639603},
title = {{Proteomic applications of automated GPCR classification.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17639603},
volume = {7},
year = {2007}
}
@article{Sgourakis2005,
abstract = {MOTIVATION: G-protein coupled receptors are a major class of eukaryotic cell-surface receptors. A very important aspect of their function is the specific interaction (coupling) with members of four G-protein families. A single GPCR may interact with members of more than one G-protein families (promiscuous coupling). To date all published methods that predict the coupling specificity of GPCRs are restricted to three main coupling groups G(i/o), G(q/11) and G(s), not including G(12/13)-coupled or other promiscuous receptors. RESULTS: We present a method that combines hidden Markov models and a feed-forward artificial neural network to overcome these limitations, while producing the most accurate predictions currently available. Using an up-to-date curated dataset, our method yields a 94\% correct classification rate in a 5-fold cross-validation test. The method predicts also promiscuous coupling preferences, including coupling to G(12/13), whereas unlike other methods avoids overpredictions (false positives) when non-GPCR sequences are encountered. AVAILABILITY: A webserver for academic users is available at http://bioinformatics.biol.uoa.gr/PRED-COUPLE2},
author = {Sgourakis, Nikolaos G and Bagos, Pantelis G and Hamodrakas, Stavros J},
doi = {10.1093/bioinformatics/bti679},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sgourakis, Bagos, Hamodrakas/2005/Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks/Sgourakis, Bagos, Hamodrakas - 2005 - Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics (Oxford, England)},
keywords = {Animals,Computational Biology,Computational Biology: methods,Computer Simulation,Computers,Databases, Genetic,False Positive Reactions,GTP-Binding Protein alpha Subunits, G12-G13,GTP-Binding Protein alpha Subunits, G12-G13: genet,GTP-Binding Protein alpha Subunits, Gi-Go,GTP-Binding Protein alpha Subunits, Gi-Go: genetic,GTP-Binding Protein alpha Subunits, Gq-G11,GTP-Binding Protein alpha Subunits, Gq-G11: geneti,GTP-Binding Protein alpha Subunits, Gs,GTP-Binding Protein alpha Subunits, Gs: genetics,GTP-Binding Proteins,GTP-Binding Proteins: genetics,Gene Library,Genes, Plant,Humans,Ligands,Markov Chains,Models, Biological,Neural Networks (Computer),Protein Binding,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: metabolism,Reproducibility of Results,Software},
month = nov,
number = {22},
pages = {4101--6},
pmid = {16174684},
title = {{Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16174684},
volume = {21},
year = {2005}
}
@article{Kall2007,
abstract = {When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65\% of all predicted signal peptides and 25-35\% of all predicted transmembrane topologies overlap. This impairs predictions of 5-10\% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius.},
author = {K\"{a}ll, Lukas and Krogh, Anders and Sonnhammer, Erik L L},
doi = {10.1093/nar/gkm256},
file = {:Users/rnowling/Documents/Mendeley Desktop/K\"{a}ll, Krogh, Sonnhammer/2007/Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server/K\"{a}ll, Krogh, Sonnhammer - 2007 - Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Computational Biology,Computational Biology: methods,Computer Simulation,Cytoplasm,Cytoplasm: metabolism,Internet,Membrane Proteins,Membrane Proteins: metabolism,Models, Molecular,Models, Theoretical,Programming Languages,Protein Conformation,Protein Sorting Signals,Protein Sorting Signals: physiology,Protein Structure, Secondary,Protein Structure, Secondary: physiology,Proteomics,Proteomics: methods,Software},
month = jul,
number = {Web Server issue},
pages = {W429--32},
pmid = {17483518},
title = {{Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933244\&tool=pmcentrez\&rendertype=abstract},
volume = {35},
year = {2007}
}
@article{Kall2004,
abstract = {An inherent problem in transmembrane protein topology prediction and signal peptide prediction is the high similarity between the hydrophobic regions of a transmembrane helix and that of a signal peptide, leading to cross-reaction between the two types of predictions. To improve predictions further, it is therefore important to make a predictor that aims to discriminate between the two classes. In addition, topology information can be gained when successfully predicting a signal peptide leading a transmembrane protein since it dictates that the N terminus of the mature protein must be on the non-cytoplasmic side of the membrane. Here, we present Phobius, a combined transmembrane protein topology and signal peptide predictor. The predictor is based on a hidden Markov model (HMM) that models the different sequence regions of a signal peptide and the different regions of a transmembrane protein in a series of interconnected states. Training was done on a newly assembled and curated dataset. Compared to TMHMM and SignalP, errors coming from cross-prediction between transmembrane segments and signal peptides were reduced substantially by Phobius. False classifications of signal peptides were reduced from 26.1\% to 3.9\% and false classifications of transmembrane helices were reduced from 19.0\% to 7.7\%. Phobius was applied to the proteomes of Homo sapiens and Escherichia coli. Here we also noted a drastic reduction of false classifications compared to TMHMM/SignalP, suggesting that Phobius is well suited for whole-genome annotation of signal peptides and transmembrane regions. The method is available at as well as at},
author = {K\"{a}ll, Lukas and Krogh, Anders and Sonnhammer, Erik L L},
doi = {10.1016/j.jmb.2004.03.016},
file = {:Users/rnowling/Documents/Mendeley Desktop/K\"{a}ll, Krogh, Sonnhammer/2004/A combined transmembrane topology and signal peptide prediction method/K\"{a}ll, Krogh, Sonnhammer - 2004 - A combined transmembrane topology and signal peptide prediction method.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Membrane Proteins,Membrane Proteins: metabolism,Models, Molecular,Protein Sorting Signals,Protein Sorting Signals: physiology,Protein Structure, Secondary,Protein Structure, Secondary: physiology},
month = may,
number = {5},
pages = {1027--36},
pmid = {15111065},
title = {{A combined transmembrane topology and signal peptide prediction method.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15111065},
volume = {338},
year = {2004}
}
@article{Krogh2001,
abstract = {We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. We present a detailed analysis of TMHMM's performance, and show that it correctly predicts 97-98 \% of the transmembrane helices. Additionally, TMHMM can discriminate between soluble and membrane proteins with both specificity and sensitivity better than 99 \%, although the accuracy drops when signal peptides are present. This high degree of accuracy allowed us to predict reliably integral membrane proteins in a large collection of genomes. Based on these predictions, we estimate that 20-30 \% of all genes in most genomes encode membrane proteins, which is in agreement with previous estimates. We further discovered that proteins with N(in)-C(in) topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans, where the large number of 7TM receptors increases the counts for N(out)-C(in) topologies. We discuss the possible relevance of this finding for our understanding of membrane protein assembly mechanisms. A TMHMM prediction service is available at http://www.cbs.dtu.dk/services/TMHMM/.},
author = {Krogh, Anders and Larsson, Bjorn and von Heijne, Gunnar and Sonnhammer, Erik L. L.},
doi = {10.1006/jmbi.2000.4315},
file = {:Users/rnowling/Documents/Mendeley Desktop/Krogh et al/2001/Predicting transmembrane protein topology with a hidden Markov model application to complete genomes/Krogh et al. - 2001 - Predicting transmembrane protein topology with a hidden Markov model application to complete genomes.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Animals,Bacterial Proteins,Bacterial Proteins: chemistry,Computational Biology,Computational Biology: methods,Databases as Topic,Fungal Proteins,Fungal Proteins: chemistry,Genome,Internet,Markov Chains,Membrane Proteins,Membrane Proteins: chemistry,Plant Proteins,Plant Proteins: chemistry,Porins,Porins: chemistry,Protein Sorting Signals,Protein Structure,Reproducibility of Results,Research Design,Secondary,Sensitivity and Specificity,Software,Solubility},
month = jan,
number = {3},
pages = {567--80},
pmid = {11152613},
title = {{Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11152613},
volume = {305},
year = {2001}
}
@article{Kitao1998,
abstract = {We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5\% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation.},
author = {Kitao, A and Hayward, S and Go, N},
file = {:Users/rnowling/Documents/Mendeley Desktop/Kitao, Hayward, Go/1998/Energy landscape of a native protein jumping-among-minima model/Kitao, Hayward, Go - 1998 - Energy landscape of a native protein jumping-among-minima model.pdf:pdf},
issn = {0887-3585},
journal = {Proteins},
keywords = {Chemical,Energy Transfer,Humans,Models,Molecular Structure,Muramidase,Muramidase: chemistry,Protein Conformation,Software},
month = dec,
number = {4},
pages = {496--517},
pmid = {9849935},
title = {{Energy landscape of a native protein: jumping-among-minima model.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9849935},
volume = {33},
year = {1998}
}
@article{Sandu1999,
author = {Sandu, Adrian and Schlick, Tamar},
doi = {10.1006/jcph.1999.6202},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sandu, Schlick/1999/Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics/Sandu, Schlick - 1999 - Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics.pdf:pdf},
issn = {00219991},
journal = {Journal of Computational Physics},
month = may,
number = {1},
pages = {74--113},
title = {{Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999199962022},
volume = {151},
year = {1999}
}
@article{Durand1994,
annote = {Initial description of block method for reduced-cost diagonalization protein Hessians.  First, residues are grouped into blocks and the 6 eigenvectors associated with rotations and translations are determined.  Secondly, the Hessian is projected onto the reduced space, diagnolized, and projected back onto full space to determine the approximate low-frequency modes. Third, the compliment of the low-frequency is found.  Lastly, a perturbation-iteration scheme is used to find the exact  low-frequency normal modes. First and second steps take O(N\^{}(9/5)) with appropriate number of blocks, while perturbation-iteration scheme is N\^{}2.},
author = {Durand, Philippe and Trinquier, Georges and Sanejouand, Y.H.},
doi = {10.1002/bip.360340608},
file = {:Users/rnowling/Documents/Mendeley Desktop/Durand, Trinquier, Sanejouand/1994/A new approach for determining low-frequency normal modes in macromolecules/Durand, Trinquier, Sanejouand - 1994 - A new approach for determining low-frequency normal modes in macromolecules.pdf:pdf},
issn = {0006-3525},
journal = {Biopolymers},
keywords = {Annotated,Diagonalization,NMA},
mendeley-tags = {Annotated,Diagonalization,NMA},
month = jun,
number = {6},
pages = {759--771},
publisher = {Wiley Online Library},
title = {{A new approach for determining low-frequency normal modes in macromolecules}},
url = {http://onlinelibrary.wiley.com/doi/10.1002/bip.360340608/abstract},
volume = {34},
year = {1994}
}
@article{Sgourakis2005a,
abstract = {BACKGROUND: G- Protein coupled receptors (GPCRs) comprise the largest group of eukaryotic cell surface receptors with great pharmacological interest. A broad range of native ligands interact and activate GPCRs, leading to signal transduction within cells. Most of these responses are mediated through the interaction of GPCRs with heterotrimeric GTP-binding proteins (G-proteins). Due to the information explosion in biological sequence databases, the development of software algorithms that could predict properties of GPCRs is important. Experimental data reported in the literature suggest that heterotrimeric G-proteins interact with parts of the activated receptor at the transmembrane helix-intracellular loop interface. Utilizing this information and membrane topology information, we have developed an intensive exploratory approach to generate a refined library of statistical models (Hidden Markov Models) that predict the coupling preference of GPCRs to heterotrimeric G-proteins. The method predicts the coupling preferences of GPCRs to Gs, Gi/o and Gq/11, but not G12/13 subfamilies. RESULTS: Using a dataset of 282 GPCR sequences of known coupling preference to G-proteins and adopting a five-fold cross-validation procedure, the method yielded an 89.7\% correct classification rate. In a validation set comprised of all receptor sequences that are species homologues to GPCRs with known coupling preferences, excluding the sequences used to train the models, our method yields a correct classification rate of 91.0\%. Furthermore, promiscuous coupling properties were correctly predicted for 6 of the 24 GPCRs that are known to interact with more than one subfamily of G-proteins. CONCLUSION: Our method demonstrates high correct classification rate. Unlike previously published methods performing the same task, it does not require any transmembrane topology prediction in a preceding step. A web-server for the prediction of GPCRs coupling specificity to G-proteins available for non-commercial users is located at http://bioinformatics.biol.uoa.gr/PRED-COUPLE.},
author = {Sgourakis, Nikolaos G and Bagos, Pantelis G and Papasaikas, Panagiotis K and Hamodrakas, Stavros J},
doi = {10.1186/1471-2105-6-104},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sgourakis et al/2005/A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models/Sgourakis et al. - 2005 - A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.pdf:pdf},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Algorithms,Amino Acid Sequence,Animals,Binding Sites,Computational Biology,Computational Biology: methods,Databases, Protein,Humans,Ligands,Markov Chains,Models, Biological,Models, Chemical,Models, Statistical,Molecular Sequence Data,Pattern Recognition, Automated,Protein Interaction Mapping,Receptors, Cell Surface,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: chemistry,Receptors, G-Protein-Coupled: genetics,Sensitivity and Specificity,Sequence Alignment,Sequence Analysis, Protein,Sequence Homology, Amino Acid,Software},
month = jan,
pages = {104},
pmid = {15847681},
title = {{A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1087828\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2005}
}
@article{Grossfield2009,
author = {Grossfield, Alan and Zuckerman, D.M.},
doi = {10.1016/S1574-1400(09)00502-7.Quantifying},
file = {:Users/rnowling/Documents/Mendeley Desktop/Grossfield, Zuckerman/2009/Quantifying uncertainty and samplying quality in biomolecular simulations/Grossfield, Zuckerman - 2009 - Quantifying uncertainty and samplying quality in biomolecular simulations.pdf:pdf},
journal = {Annual reports in computational chemistry},
keywords = {block averaging,convergence,error analysis,principal component},
number = {09},
pages = {23--48},
publisher = {Elsevier},
title = {{Quantifying uncertainty and samplying quality in biomolecular simulations}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1574140009005027},
volume = {5},
year = {2009}
}
@article{Lyman2006,
abstract = {Assessing the convergence of a biomolecular simulation is an essential part of any careful computational investigation, because many fundamental aspects of molecular behavior depend on the relative populations of different conformers. Here we present a physically intuitive method to self-consistently assess the convergence of trajectories generated by molecular dynamics and related methods. Our approach reports directly and systematically on the structural diversity of a simulation trajectory. Straightforward clustering and classification steps are the key ingredients, allowing the approach to be trivially applied to systems of any size. Our initial study on met-enkephalin strongly suggests that even fairly long trajectories (approximately 50 ns) may not be converged for this small--but highly flexible--system.},
author = {Lyman, Edward and Zuckerman, Daniel M},
doi = {10.1529/biophysj.106.082941},
file = {:Users/rnowling/Documents/Mendeley Desktop/Lyman, Zuckerman/2006/Ensemble-based convergence analysis of biomolecular trajectories/Lyman, Zuckerman - 2006 - Ensemble-based convergence analysis of biomolecular trajectories.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Biopolymers,Biopolymers: chemistry,Computer Simulation,Elasticity,Models, Chemical,Models, Molecular,Motion,Multiprotein Complexes,Multiprotein Complexes: chemistry,Multiprotein Complexes: ultrastructure,Protein Conformation,Proteins,Proteins: chemistry,Proteins: ultrastructure,Stress, Mechanical},
month = jul,
number = {1},
pages = {164--72},
pmid = {16617086},
publisher = {Elsevier},
title = {{Ensemble-based convergence analysis of biomolecular trajectories.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1479051\&tool=pmcentrez\&rendertype=abstract},
volume = {91},
year = {2006}
}
@article{Zhang2007,
abstract = {The computational sampling of rare, large-scale, conformational transitions in proteins is a well appreciated challenge-for which a number of potentially efficient path-sampling methodologies have been proposed. Here, we study a large-scale transition in a united-residue model of calmodulin using the "weighted ensemble" (WE) approach of Huber and Kim. Because of the model's relative simplicity, we are able to compare our results with brute-force simulations. The comparison indicates that the WE approach quantitatively reproduces the brute-force results, as assessed by considering (i) the reaction rate, (ii) the distribution of event durations, and (iii) structural distributions describing the heterogeneity of the paths. Importantly, the WE method is readily applied to more chemically accurate models, and by studying a series of lower temperatures, our results suggest that the WE method can increase efficiency by orders of magnitude in more challenging systems.},
author = {Zhang, Bin W and Jasnow, David and Zuckerman, Daniel M},
doi = {10.1073/pnas.0706349104},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zhang, Jasnow, Zuckerman/2007/Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin/Zhang, Jasnow, Zuckerman - 2007 - Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Calmodulin,Calmodulin: chemistry,Kinetics,Models, Molecular,Protein Conformation},
month = nov,
number = {46},
pages = {18043--8},
pmid = {17984047},
title = {{Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2084293\&tool=pmcentrez\&rendertype=abstract},
volume = {104},
year = {2007}
}
@article{Lyman2007,
abstract = {Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of simulation trajectories has remained difficult to assess. Such assessment is critical not only for establishing the relevance of any individual simulation but also in the extremely active field of developing computational methods. Here we map the trajectory assessment problem onto a simple statistical calculation of the "effective sample size", that is, the number of statistically independent configurations. The mapping is achieved by asking the question, "How much time must elapse between snapshots included in a sample for that sample to exhibit the statistical properties expected for independent and identically distributed configurations?" Our method is more general than autocorrelation methods in that it directly probes the configuration-space distribution without requiring a priori definition of configurational substates and without any fitting parameters. We show that the method is equally and directly applicable to toy models, peptides, and a 72-residue protein model. Variants of our approach can readily be applied to a wide range of physical and chemical systems.},
author = {Lyman, Edward and Zuckerman, Daniel M},
doi = {10.1021/jp073061t},
file = {:Users/rnowling/Documents/Mendeley Desktop/Lyman, Zuckerman/2007/On the structural convergence of biomolecular simulations by determination of the effective sample size/Lyman, Zuckerman - 2007 - On the structural convergence of biomolecular simulations by determination of the effective sample size.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
keywords = {Calmodulin,Calmodulin: chemistry,Computer Simulation,Dipeptides,Dipeptides: chemistry,Enkephalin, Methionine,Enkephalin, Methionine: chemistry,Leucine,Leucine: chemistry,Models, Chemical,Models, Statistical,Sample Size},
month = nov,
number = {44},
pages = {12876--82},
pmid = {17935314},
title = {{On the structural convergence of biomolecular simulations by determination of the effective sample size.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2538559\&tool=pmcentrez\&rendertype=abstract},
volume = {111},
year = {2007}
}
@article{Wu1998,
author = {Wu, Xiongwu and Wang, Shaomeng},
doi = {10.1021/jp9817372},
file = {:Users/rnowling/Documents/Mendeley Desktop/Wu, Wang/1998/Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search/Wu, Wang - 1998 - Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search.pdf:pdf},
issn = {1520-6106},
journal = {The Journal of Physical Chemistry B},
month = sep,
number = {37},
pages = {7238--7250},
title = {{Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search}},
url = {http://pubs.acs.org/doi/abs/10.1021/jp9817372},
volume = {102},
year = {1998}
}
@article{Wu2003,
author = {Wu, Xiongwu and Brooks, Bernard R.},
doi = {10.1016/j.cplett.2003.10.013},
file = {:Users/rnowling/Documents/Mendeley Desktop/Wu, Brooks/2003/Self-guided Langevin dynamics simulation method/Wu, Brooks - 2003 - Self-guided Langevin dynamics simulation method.pdf:pdf},
issn = {00092614},
journal = {Chemical Physics Letters},
month = nov,
number = {3-4},
pages = {512--518},
title = {{Self-guided Langevin dynamics simulation method}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009261403017585},
volume = {381},
year = {2003}
}
@article{Berne1997,
abstract = {New advances in molecular dynamics and Monte Carlo simulations have led to impressive increases in the speed of sampling phase space for complex biological systems. These methods have been combined with new fast algorithms for computing long range electrostatic interactions for new polarizable force fields. In addition, new methods for sampling low energy molecular conformations allow the rapid determination of thermodynamically dominant regions on the potential-energy surface. Accurate measures of the rate of phase-space sampling should allow both the optimization and the comparison of methods for a particular problem of interest.},
author = {Berne, Bruce J and Straub, John E},
file = {:Users/rnowling/Documents/Mendeley Desktop/Berne, Straub/1997/Novel methods of sampling phase space in the simulation of biological systems/Berne, Straub - 1997 - Novel methods of sampling phase space in the simulation of biological systems.pdf:pdf},
issn = {0959-440X},
journal = {Current opinion in structural biology},
keywords = {Algorithms,Models,Molecular,Monte Carlo Method,Static Electricity},
month = apr,
number = {2},
pages = {181--9},
pmid = {9094324},
title = {{Novel methods of sampling phase space in the simulation of biological systems.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9094324},
volume = {7},
year = {1997}
}
@article{Thirumalai1989,
author = {Thirumalai, D. and Mountain, R.D. and Kirkpatrick, TR},
file = {:Users/rnowling/Documents/Mendeley Desktop/Thirumalai, Mountain, Kirkpatrick/1989/Ergodic behavior in supercooled liquids and in glasses/Thirumalai, Mountain, Kirkpatrick - 1989 - Ergodic behavior in supercooled liquids and in glasses.pdf:pdf},
journal = {Physical Review A},
number = {7},
pages = {3563},
publisher = {APS},
title = {{Ergodic behavior in supercooled liquids and in glasses}},
url = {http://pra.aps.org/abstract/PRA/v39/i7/p3563\_1},
volume = {39},
year = {1989}
}
@article{Zhou1997,
author = {Zhou, Ruhong and Berne, BJ},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zhou, Berne/1997/Smart walking A new method for Boltzmann sampling of protein conformations/Zhou, Berne - 1997 - Smart walking A new method for Boltzmann sampling of protein conformations.pdf:pdf},
journal = {The Journal of chemical physics},
number = {21},
pages = {9185},
title = {{Smart walking: A new method for Boltzmann sampling of protein conformations}},
url = {http://link.aip.org/link/?JCPSA6/107/9185/1},
volume = {107},
year = {1997}
}
@article{Schlick2009,
abstract = {The rugged energy landscape of biomolecules and associated large-scale conformational changes have triggered the development of many innovative enhanced sampling methods, either based or not based on molecular dynamics (MD) simulations. Surveyed here are methods in the latter class - including Monte Carlo methods, harmonic approximations, and coarse graining - many of which yield valuable conformational insights into biomolecular structure and flexibility, despite altered kinetics. MD-based methods are surveyed in an upcoming issue of F1000 Biology Reports.},
author = {Schlick, Tamar},
doi = {10.3410/B1-48},
file = {:Users/rnowling/Documents/Mendeley Desktop/Schlick/2009/Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure/Schlick - 2009 - Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure.pdf:pdf},
issn = {1757-594X},
journal = {F1000 biology reports},
month = jan,
number = {June},
pmid = {20948637},
title = {{Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2924683\&tool=pmcentrez\&rendertype=abstract},
volume = {1},
year = {2009}
}
@article{Schlick2009a,
abstract = {The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational changes along with chemical dynamics behavior. In this report, MD-based methods for biomolecules are surveyed, involving modification of the potential, simulation protocol, or algorithm as well as global reformulations. While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov chain models are required to obtain mechanistic information, reaction pathways, and/or reaction rates. Divide-and-conquer methods for sampling and for piecing together reaction rate information are especially suitable for readily available computer cluster networks. Successful applications to biomolecules remain a challenge.},
author = {Schlick, Tamar},
doi = {10.3410/B1-51},
file = {:Users/rnowling/Documents/Mendeley Desktop/Schlick/2009/Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules/Schlick - 2009 - Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.pdf:pdf},
issn = {1757-594X},
journal = {F1000 biology reports},
month = jan,
number = {July},
pmid = {20948633},
title = {{Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2948272\&tool=pmcentrez\&rendertype=abstract},
volume = {1},
year = {2009}
}
@article{Schlick2011,
abstract = {We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field's history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.},
author = {Schlick, Tamar and Collepardo-Guevara, Rosana and Halvorsen, Leif Arthur and Jung, Segun and Xiao, Xia},
doi = {10.1017/S0033583510000284},
file = {:Users/rnowling/Documents/Mendeley Desktop/Schlick et al/2011/Biomolecular modeling and simulation a field coming of age/Schlick et al. - 2011 - Biomolecular modeling and simulation a field coming of age.pdf:pdf},
issn = {1469-8994},
journal = {Quarterly reviews of biophysics},
month = jan,
pages = {1--38},
pmid = {21226976},
title = {{Biomolecular modeling and simulation: a field coming of age.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21226976},
volume = {2},
year = {2011}
}
@article{Darve2009,
abstract = {The Mori-Zwanzig formalism is an effective tool to derive differential equations describing the evolution of a small number of resolved variables. In this paper we present its application to the derivation of generalized Langevin equations and generalized non-Markovian Fokker-Planck equations. We show how long time scales rates and metastable basins can be extracted from these equations. Numerical algorithms are proposed to discretize these equations. An important aspect is the numerical solution of the orthogonal dynamics equation which is a partial differential equation in a high dimensional space. We propose efficient numerical methods to solve this orthogonal dynamics equation. In addition, we present a projection formalism of the Mori-Zwanzig type that is applicable to discrete maps. Numerical applications are presented from the field of Hamiltonian systems.},
author = {Darve, Eric and Solomon, Jose and Kia, Amirali},
doi = {10.1073/pnas.0902633106},
file = {:Users/rnowling/Documents/Mendeley Desktop/Darve, Solomon, Kia/2009/Computing generalized Langevin equations and generalized Fokker-Planck equations/Darve, Solomon, Kia - 2009 - Computing generalized Langevin equations and generalized Fokker-Planck equations.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
month = jul,
number = {27},
pages = {10884--9},
pmid = {19549838},
title = {{Computing generalized Langevin equations and generalized Fokker-Planck equations.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2708778\&tool=pmcentrez\&rendertype=abstract},
volume = {106},
year = {2009}
}
@inproceedings{Izaguirre2010,
author = {Izaguirre, J.A. and Sweet, C.R. and Pande, V.S.},
booktitle = {Pacific Symposium on Biocomputing},
file = {:Users/rnowling/Documents/Mendeley Desktop/Izaguirre, Sweet, Pande/2010/Multiscale Dynamics of Macromolecules Using Normal Mode Langevin/Izaguirre, Sweet, Pande - 2010 - Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.pdf:pdf},
keywords = {langevin dynamics,multiscale integrators,normal mode dynamics},
pages = {240},
title = {{Multiscale Dynamics of Macromolecules Using Normal Mode Langevin}},
url = {http://eproceedings.worldscinet.com/9789814295291/preserved-docs/9789814295291\_0026.pdf},
year = {2010}
}
@article{Morrone2010,
author = {Morrone, Joseph a. and Zhou, Ruhong and Berne, B. J.},
doi = {10.1021/ct100054k},
file = {:Users/rnowling/Documents/Mendeley Desktop/Morrone, Zhou, Berne/2010/Molecular Dynamics with Multiple Time Scales How to Avoid Pitfalls/Morrone, Zhou, Berne - 2010 - Molecular Dynamics with Multiple Time Scales How to Avoid Pitfalls.pdf:pdf},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
month = jun,
number = {6},
pages = {1798--1804},
title = {{Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls}},
url = {http://pubs.acs.org/doi/abs/10.1021/ct100054k},
volume = {6},
year = {2010}
}
@article{Sweet2008,
abstract = {We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. Our basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which have a physical meaning of being the square of the mode frequency. Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. In NML, the higher frequency modes are overdamped and relaxed near their energy minimum while respecting the subspace of low frequency dynamical modes. Our numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30\% of the modes propagated, when compared to the full model. For implicitly solvated systems, NML gives a twofold improvement in efficiency over plain Langevin dynamics for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for sampling an 882 atom (bovine pancreatic trypsin inhibitor) model, with good scaling with system size subject to the number of modes propagated. NML has been implemented in the open source software PROTOMOL.},
author = {Sweet, Christopher R and Petrone, Paula and Pande, Vijay S and Izaguirre, Jes\'{u}s A},
doi = {10.1063/1.2883966},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sweet et al/2008/Normal mode partitioning of Langevin dynamics for biomolecules/Sweet et al. - 2008 - Normal mode partitioning of Langevin dynamics for biomolecules.pdf:pdf},
issn = {0021-9606},
journal = {The Journal of chemical physics},
keywords = {Algorithms,Biopolymers,Biopolymers: chemistry,Chemical,Computer Simulation,Models,Molecular,Molecular Conformation},
month = apr,
number = {14},
pages = {145101},
pmid = {18412479},
title = {{Normal mode partitioning of Langevin dynamics for biomolecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18412479},
volume = {128},
year = {2008}
}
@article{Kottalam1986,
abstract = {Langevin modes describe the behavior of atoms moving on a harmonic potential surface subject to viscous damping described by a classical Langevin equation. We present applications to the protein crambin and to the DNA duplex d(CpGpCpGpCpG)2 and its complex with ethidium. Our friction matrix is weighted according to surface area exposed to solvent, and results are reported for various values of the solvent viscosity and models for hydrodynamic interactions. Even for relatively small solvent friction (eta = 0.3 cp) a substantial number of modes are overdamped, and time correlation functions decay smoothly without the oscillations characteristic of gas-phase calculations. Perturbation theory starting from the gas-phase modes is accurate for many low-frequency modes (which are overdamped in the presence of solvent), but fails badly for higher modes. For correlation functions of interest to fluorescence depolarization or nmr relaxation, the plateau values are insensitive to solvent viscosity, but the relaxation times are not. The advantages and limitations of this analysis of macromolecular motions are discussed.},
author = {Kottalam, J and Case, D a},
doi = {10.1002/bip.360291008},
file = {:Users/rnowling/Documents/Mendeley Desktop/Kottalam, Case/1986/Langevin modes of macromolecules applications to crambin and DNA hexamers/Kottalam, Case - 1986 - Langevin modes of macromolecules applications to crambin and DNA hexamers.pdf:pdf},
issn = {0006-3525},
journal = {Biopolymers},
keywords = {DNA,Macromolecular Substances,Mathematics,Oligodeoxyribonucleotides,Plant Proteins,Viscosity},
number = {10-11},
pages = {1409--21},
pmid = {2361153},
title = {{Langevin modes of macromolecules: applications to crambin and DNA hexamers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2361153},
volume = {29},
year = {1986}
}
@article{Shaw2010a,
author = {Shaw, D. E. and Maragakis, P. and Lindorff-Larsen, K. and Piana, S. and Dror, R. O. and Eastwood, M. P. and Bank, J. a. and Jumper, J. M. and Salmon, J. K. and Shan, Y. and Wriggers, W.},
doi = {10.1126/science.1187409},
file = {:Users/rnowling/Documents/Mendeley Desktop/Shaw et al/2010/Atomic-Level Characterization of the Structural Dynamics of Proteins/Shaw et al. - 2010 - Atomic-Level Characterization of the Structural Dynamics of Proteins.pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = oct,
number = {6002},
pages = {341--346},
title = {{Atomic-Level Characterization of the Structural Dynamics of Proteins}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1187409},
volume = {330},
year = {2010}
}
@article{Halko2011,
author = {Halko, N and Martinsson, P G and Tropp, J A},
file = {:Users/rnowling/Documents/Mendeley Desktop/Halko, Martinsson, Tropp/2011/Finding Structure with Randomness Probabilistic Algorithms for Matrix Decompositions ∗ Part I Introduction/Halko, Martinsson, Tropp - 2011 - Finding Structure with Randomness Probabilistic Algorithms for Matrix Decompositions ∗ Part I Introduction.pdf:pdf},
journal = {Society},
keywords = {dimension reduction,eigenvalue decomposition,factorization,interpolative decomposition,johnson,lindenstrauss lemma,matrix approximation,parallel algorithm,pass-efficient algorithm,principal component analysis,random matrix,randomized algorithm,rank-revealing qr,singular value decomposition,streaming algorithm},
number = {2},
pages = {217--288},
title = {{Finding Structure with Randomness : Probabilistic Algorithms for Matrix Decompositions ∗ Part I : Introduction}},
volume = {53},
year = {2011}
}
@article{Bajaj2011,
author = {Bajaj, Chandrahit and Chen, Shun-Chuan and Rand, Alexander},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bajaj, Chen, Rand/2011/An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson – Boltzmann-Based Molecular Electrostatics/Bajaj, Chen, Rand - 2011 - An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson – Boltzmann-Based Molecular Electrostatics.pdf:pdf},
journal = {SIAM Journal on Scientific Computing},
keywords = {090764645,1,10,1137,65n38,92c40,ams subject classifications,boltzmann equation,boundary element method,doi,energy are often used,fast multipole method,in biol-,introduction,models of molecular potential,poisson},
number = {2},
pages = {826},
title = {{An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson – Boltzmann-Based Molecular Electrostatics}},
url = {http://link.aip.org/link/?SJOCE3/33/826/1},
volume = {33},
year = {2011}
}
@article{Kallemov2011,
author = {Kallemov, Bakytzhan and Miller, G.H.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Kallemov, Miller/2011/A Second-order Strong Method for the Langevin Equations with Holonomic Constraints/Kallemov, Miller - 2011 - A Second-order Strong Method for the Langevin Equations with Holonomic Constraints.pdf:pdf},
journal = {SIAM Journal on Scientific Computing},
keywords = {10,100785600,1137,58j65,60h10,65l07,82c31,ams subject classifications,doi,equations,langevin,multiple stochastic integrals,ornstein,stochastic particle dynamics,strong order,uhlenbeck process},
number = {2},
pages = {653},
title = {{A Second-order Strong Method for the Langevin Equations with Holonomic Constraints}},
url = {http://link.aip.org/link/?SJOCE3/33/653/1},
volume = {33},
year = {2011}
}
@article{Huang2008,
abstract = {We have implemented the serial replica exchange method (SREM) and simulated tempering (ST) enhanced sampling algorithms in a global distributed computing environment. Here we examine the helix-coil transition of a 21 residue alpha-helical peptide in explicit solvent. For ST, we demonstrate the efficacy of a new method for determining initial weights allowing the system to perform a random walk in temperature space based on short trial simulations. These weights are updated throughout the production simulation by an adaptive weighting method. We give a detailed comparison of SREM, ST, as well as standard MD and find that SREM and ST give equivalent results in reasonable agreement with experimental data. In addition, we find that both enhanced sampling methods are much more efficient than standard MD simulations. The melting temperature of the Fs peptide with the AMBER99phi potential was calculated to be about 310 K, which is in reasonable agreement with the experimental value of 334 K. We also discuss other temperature dependent properties of the helix-coil transition. Although ST has certain advantages over SREM, both SREM and ST are shown to be powerful methods via distributed computing and will be applied extensively in future studies of complex bimolecular systems.},
author = {Huang, Xuhui and Bowman, Gregory R and Pande, Vijay S},
doi = {10.1063/1.2908251},
file = {:Users/rnowling/Documents/Mendeley Desktop/Huang, Bowman, Pande/2008/Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment/Huang, Bowman, Pande - 2008 - Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Algorithms,Amino Acid Sequence,Computer Simulation,Models, Molecular,Molecular Sequence Data,Peptides,Peptides: chemistry,Peptides: metabolism,Protein Folding,Protein Structure, Secondary,Temperature,Thermodynamics},
month = may,
number = {20},
pages = {205106},
pmid = {18513049},
title = {{Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2809694\&tool=pmcentrez\&rendertype=abstract},
volume = {128},
year = {2008}
}
@article{Huang2009,
abstract = {Simulating the conformational dynamics of biomolecules is extremely difficult due to the rugged nature of their free energy landscapes and multiple long-lived, or metastable, states. Generalized ensemble (GE) algorithms, which have become popular in recent years, attempt to facilitate crossing between states at low temperatures by inducing a random walk in temperature space. Enthalpic barriers may be crossed more easily at high temperatures; however, entropic barriers will become more significant. This poses a problem because the dominant barriers to conformational change are entropic for many biological systems, such as the short RNA hairpin studied here. We present a new efficient algorithm for conformational sampling, called the adaptive seeding method (ASM), which uses nonequilibrium GE simulations to identify the metastable states, and seeds short simulations at constant temperature from each of them to quantitatively determine their equilibrium populations. Thus, the ASM takes advantage of the broad sampling possible with GE algorithms but generally crosses entropic barriers more efficiently during the seeding simulations at low temperature. We show that only local equilibrium is necessary for ASM, so very short seeding simulations may be used. Moreover, the ASM may be used to recover equilibrium properties from existing datasets that failed to converge, and is well suited to running on modern computer clusters.},
author = {Huang, Xuhui and Bowman, Gregory R and Bacallado, Sergio and Pande, Vijay S},
doi = {10.1073/pnas.0909088106},
file = {:Users/rnowling/Documents/Mendeley Desktop/Huang et al/2009/Rapid equilibrium sampling initiated from nonequilibrium data/Huang et al. - 2009 - Rapid equilibrium sampling initiated from nonequilibrium data.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Algorithms,Markov Chains,Models, Molecular,Molecular Dynamics Simulation,Thermodynamics},
month = nov,
number = {47},
pages = {19765--9},
pmid = {19805023},
title = {{Rapid equilibrium sampling initiated from nonequilibrium data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2785240\&tool=pmcentrez\&rendertype=abstract},
volume = {106},
year = {2009}
}
@article{Bahar2010a,
abstract = {Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.},
author = {Bahar, Ivet and Lezon, Timothy R and Yang, Lee-Wei and Eyal, Eran},
doi = {10.1146/annurev.biophys.093008.131258},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bahar et al/2010/Global dynamics of proteins bridging between structure and function/Bahar et al. - 2010 - Global dynamics of proteins bridging between structure and function.pdf:pdf},
issn = {1936-1238},
journal = {Annual review of biophysics},
keywords = {allosteric changes in conformation,closed,collective motions,elastic network models,normal modes,open,principal component analysis},
month = jun,
pages = {23--42},
pmid = {20192781},
title = {{Global dynamics of proteins: bridging between structure and function.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20192781},
volume = {39},
year = {2010}
}
@article{Mitsutake2003,
author = {Mitsutake, Ayori and Sugita, Yuji and Okamoto, Yuko},
doi = {10.1063/1.1555847},
file = {:Users/rnowling/Documents/Mendeley Desktop/Mitsutake, Sugita, Okamoto/2003/Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test/Mitsutake, Sugita, Okamoto - 2003 - Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test.pdf:pdf},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {14},
pages = {6664},
title = {{Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test}},
url = {http://link.aip.org/link/JCPSA6/v118/i14/p6664/s1\&Agg=doi},
volume = {118},
year = {2003}
}
@article{Hansmann1996,
author = {Hansmann, Ulrich H.E. and Okamoto, Yuko and Eisenmenger, Frank},
doi = {10.1016/0009-2614(96)00761-0},
file = {:Users/rnowling/Documents/Mendeley Desktop/Hansmann, Okamoto, Eisenmenger/1996/Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble/Hansmann, Okamoto, Eisenmenger - 1996 - Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble.pdf:pdf},
issn = {0009-2614},
journal = {Chemical physics letters},
month = sep,
number = {3-4},
pages = {321--330},
publisher = {Elsevier},
title = {{Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0009261496007610},
volume = {259},
year = {1996}
}
@article{Sugita1999,
abstract = {Understanding protein folding is one of the most challenging problems remaining in molecular biology. In this chapter, a highly parallel replica exchange molecular dynamics (REMD) method and its application to protein folding are described. The REMD method couples molecular dynamics trajectories with a temperature exchange Monte Carlo process for efficient sampling of the conformational space. A series of replicas are run in parallel at temperatures ranging from the desired temperature to a high temperature at which the replica can easily surmount the energy barriers. From time to time the configurations of neighboring replicas are exchanged and this exchange is accepted or rejected based on a Metropolis acceptance criterion that guarantees the detailed balance. Two example protein systems, one alpha-helix and one beta-hairpin, are used as case studies to demonstrate the power of the algorithm. Up to 64 replicas of solvated protein systems are simulated in parallel over a wide range of temperatures. The simulation results show that the combined trajectories in temperature and configurational space allow a replica to overcome free energy barriers present at low temperatures. These large-scale simulations also reveal detailed results on folding mechanisms, intermediate state structures, thermodynamic properties, and the temperature dependences for both protein systems.},
author = {Sugita, Yuji and Okamoto, Yuko},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sugita, Okamoto/1999/Replica-exchange molecular dynamics method for protein folding/Sugita, Okamoto - 1999 - Replica-exchange molecular dynamics method for protein folding.pdf:pdf},
issn = {0009-2614},
journal = {Chemical Physics Letters},
keywords = {Algorithms,Chemical,Computer Simulation,Models,Monte Carlo Method,Protein Conformation,Protein Folding,Proteins,Proteins: chemistry,Temperature},
month = jan,
number = {1-2},
pages = {141--151},
pmid = {16957325},
publisher = {Elsevier},
title = {{Replica-exchange molecular dynamics method for protein folding}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009261499011239},
volume = {314},
year = {1999}
}
@article{Earl2005,
abstract = {We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physicochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering, and we suggest several promising avenues for future research.},
author = {Earl, David J and Deem, Michael W},
file = {:Users/rnowling/Documents/Mendeley Desktop/Earl, Deem/2005/Parallel tempering theory, applications, and new perspectives/Earl, Deem - 2005 - Parallel tempering theory, applications, and new perspectives.pdf:pdf},
issn = {1463-9076},
journal = {Physical chemistry chemical physics : PCCP},
keywords = {Amino Acids,Amino Acids: chemistry,Biocompatible Materials,Biocompatible Materials: chemistry,Biophysics,Biophysics: methods,Chemistry, Physical,Chemistry, Physical: methods,Computer Simulation,Models, Statistical,Models, Theoretical,Monte Carlo Method,Peptides,Peptides: chemistry,Polymers,Polymers: chemistry,Proteins,Proteins: chemistry,Quantum Theory,Temperature},
month = dec,
number = {23},
pages = {3910--6},
pmid = {19810318},
title = {{Parallel tempering: theory, applications, and new perspectives.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19810318},
volume = {7},
year = {2005}
}
@article{Hansmann1997,
author = {Hansmann, Ulrich H.E.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Hansmann/1997/Parallel Tempering Algorithm for Conformational Studies of Biological Molecules/Hansmann - 1997 - Parallel Tempering Algorithm for Conformational Studies of Biological Molecules.pdf:pdf},
issn = {0009-2614},
journal = {Chemical Physics Letters},
number = {1-3},
pages = {140--150},
publisher = {Elsevier},
title = {{Parallel Tempering Algorithm for Conformational Studies of Biological Molecules}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009261497011986},
volume = {281},
year = {1997}
}
@article{Izaguirre2004,
author = {Izaguirre, J.A. and Hampton, S.S.},
doi = {10.1016/j.jcp.2004.04.016},
file = {:Users/rnowling/Documents/Mendeley Desktop/Izaguirre, Hampton/2004/Shadow hybrid Monte Carlo an efficient propagator in phase space of macromolecules/Izaguirre, Hampton - 2004 - Shadow hybrid Monte Carlo an efficient propagator in phase space of macromolecules.pdf:pdf},
issn = {0021-9991},
journal = {Journal of Computational Physics},
keywords = {conformational sampling,hybrid monte carlo,modified hamiltonian,sampling methods,symplectic integrator},
month = nov,
number = {2},
pages = {581--604},
publisher = {Elsevier},
title = {{Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0021999104001809},
volume = {200},
year = {2004}
}
@article{Kim2010,
abstract = {We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weight and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters. Illustrative simulations on Potts spins with varying system size and simulation conditions demonstrate a comprehensive sampling for phase-coexistent states with a dramatic acceleration of tunneling transitions. A significant improvement over the power-law slowing down of mean tunneling times with increasing system size is obtained, and the underlying mechanism for accelerated tunneling is discussed.},
author = {Kim, Jaegil and Keyes, Thomas and Straub, John E},
doi = {10.1063/1.3432176},
file = {:Users/rnowling/Documents/Mendeley Desktop/Kim, Keyes, Straub/2010/Generalized replica exchange method/Kim, Keyes, Straub - 2010 - Generalized replica exchange method.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
month = jun,
number = {22},
pages = {224107},
pmid = {20550390},
title = {{Generalized replica exchange method.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20550390},
volume = {132},
year = {2010}
}
@article{Sweet2009,
abstract = {Hybrid Monte Carlo (HMC) is a rigorous sampling method that uses molecular dynamics (MD) as a global Monte Carlo move. The acceptance rate of HMC decays exponentially with system size. The shadow hybrid Monte Carlo (SHMC) was previously introduced to reduce this performance degradation by sampling instead from the shadow Hamiltonian defined for MD when using a symplectic integrator. SHMC's performance is limited by the need to generate momenta for the MD step from a nonseparable shadow Hamiltonian. We introduce the separable shadow Hamiltonian hybrid Monte Carlo (S2HMC) method based on a formulation of the leapfrog/Verlet integrator that corresponds to a separable shadow Hamiltonian, which allows efficient generation of momenta. S2HMC gives the acceptance rate of a fourth order integrator at the cost of a second-order integrator. Through numerical experiments we show that S2HMC consistently gives a speedup greater than two over HMC for systems with more than 4000 atoms for the same variance. By comparison, SHMC gave a maximum speedup of only 1.6 over HMC. S2HMC has the additional advantage of not requiring any user parameters beyond those of HMC. S2HMC is available in the program PROTOMOL 2.1. A Python version, adequate for didactic purposes, is also in MDL (http://mdlab.sourceforge.net/s2hmc).},
author = {Sweet, Christopher R and Hampton, Scott S and Skeel, Robert D and Izaguirre, Jes\'{u}s a},
doi = {10.1063/1.3253687},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sweet et al/2009/A separable shadow Hamiltonian hybrid Monte Carlo method/Sweet et al. - 2009 - A separable shadow Hamiltonian hybrid Monte Carlo method.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Molecular Dynamics Simulation,Monte Carlo Method,Thermodynamics,Water,Water: chemistry},
month = nov,
number = {17},
pages = {174106},
pmid = {19894997},
title = {{A separable shadow Hamiltonian hybrid Monte Carlo method.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2787059\&tool=pmcentrez\&rendertype=abstract},
volume = {131},
year = {2009}
}
@article{Kim2009,
abstract = {The replica exchange statistical temperature Monte Carlo algorithm (RESTMC) is presented, extending the single-replica STMC algorithm [J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 97, 050601 (2006)] to alleviate the slow convergence of the conventional temperature replica exchange method (t-REM) with increasing system size. In contrast to the Gibbs-Boltzmann sampling at a specific temperature characteristic of the standard t-REM, RESTMC samples a range of temperatures in each replica and achieves a flat energy sampling employing the generalized sampling weight, which is automatically determined via the dynamic modification of the replica-dependent statistical temperature. Faster weight determination, through the dynamic update of the statistical temperature, and the flat energy sampling, maximizing energy overlaps between neighboring replicas, lead to a considerable acceleration in the convergence of simulations even while employing significantly fewer replicas. The performance of RESTMC is demonstrated and quantitatively compared with that of the conventional t-REM under varying simulation conditions for Lennard-Jones 19, 31, and 55 atomic clusters, exhibiting single- and double-funneled energy landscapes.},
author = {Kim, Jaegil and Keyes, Thomas and Straub, John E},
doi = {10.1063/1.3095422},
file = {:Users/rnowling/Documents/Mendeley Desktop/Kim, Keyes, Straub/2009/Replica exchange statistical temperature Monte Carlo/Kim, Keyes, Straub - 2009 - Replica exchange statistical temperature Monte Carlo.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Algorithms,Models, Chemical,Monte Carlo Method,Temperature,Thermodynamics},
month = mar,
number = {12},
pages = {124112},
pmid = {19334813},
title = {{Replica exchange statistical temperature Monte Carlo.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2736574\&tool=pmcentrez\&rendertype=abstract},
volume = {130},
year = {2009}
}
@article{Sindhikara2008,
abstract = {The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.},
author = {Sindhikara, Daniel and Meng, Yilin and Roitberg, Adrian E},
doi = {10.1063/1.2816560},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sindhikara, Meng, Roitberg/2008/Exchange frequency in replica exchange molecular dynamics/Sindhikara, Meng, Roitberg - 2008 - Exchange frequency in replica exchange molecular dynamics.pdf:pdf},
issn = {0021-9606},
journal = {The Journal of chemical physics},
keywords = {Computer Simulation,Peptides,Peptides: chemistry,Protein Conformation,Thermodynamics},
month = jan,
number = {2},
pages = {024103},
pmid = {18205439},
title = {{Exchange frequency in replica exchange molecular dynamics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18205439},
volume = {128},
year = {2008}
}
@article{Brenner2007,
abstract = {The authors accelerate the replica exchange method through an efficient all-pairs replica exchange. A proof of detailed balance is shown along with an analytical estimate of the enhanced exchange efficiency. The new method provides asymptotically four fold speedup of conformation traversal for replica counts of 8 and larger with typical exchange rates. Experimental tests using the blocked alanine dipeptide demonstrate the method's correctness and show an approximate sampling efficiency improvement of 100\% according to potential energy cumulative averages and an ergodic measure. An explicitly solvated PIN1 WW domain system of 4958 atoms is sampled using our new method, yielding a cluster sampling rate almost twice that of the single exchange near neighbor implementation. Computational software and scripts along with input and output data sets are available at.},
author = {Brenner, Paul and Sweet, Christopher R and VonHandorf, Dustin and Izaguirre, Jes\'{u}s a},
doi = {10.1063/1.2436872},
file = {:Users/rnowling/Documents/Mendeley Desktop/Brenner et al/2007/Accelerating the replica exchange method through an efficient all-pairs exchange/Brenner et al. - 2007 - Accelerating the replica exchange method through an efficient all-pairs exchange.pdf:pdf},
issn = {0021-9606},
journal = {The Journal of chemical physics},
keywords = {Algorithms,Computer Simulation,Dipeptides,Dipeptides: chemistry,Models, Chemical,Models, Molecular,Peptidylprolyl Isomerase,Peptidylprolyl Isomerase: chemistry,Protein Conformation,Protein Structure, Tertiary,Proteins,Proteins: chemistry},
month = feb,
number = {7},
pages = {074103},
pmid = {17328589},
title = {{Accelerating the replica exchange method through an efficient all-pairs exchange.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17328589},
volume = {126},
year = {2007}
}
@article{Bashor2010,
abstract = {The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems. Expected final online publication date for the Annual Review of Biophysics Volume 39 is May 05, 2010. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.},
author = {Bashor, Caleb J and Horwitz, Andrew a and Peisajovich, Sergio G and Lim, Wendell a},
doi = {10.1146/annurev.biophys.050708.133652},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bashor et al/2010/Rewiring Cells Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems/Bashor et al. - 2010 - Rewiring Cells Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems.pdf:pdf},
issn = {1936-1238},
journal = {Annual review of biophysics},
keywords = {engineering,evolvability,modularity,network},
month = feb,
pmid = {20192780},
title = {{Rewiring Cells: Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20192780},
year = {2010}
}
@article{Thirumalai2010,
abstract = {Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and timescales of folding are, to a large extent, determined by N, the number of residues. The intricate details of folding as a function of denaturant concentration can be predicted by using a novel coarse-grained molecular transfer model. By watching one molecule fold at a time, using single-molecule methods, investigators have established the validity of the theoretically anticipated heterogeneity in the folding routes and the N-dependent timescales for the three stages in the approach to the native state. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the protein folding problem in the broadest sense. Expected final online publication date for the Annual Review of Biophysics Volume 39 is May 05, 2010. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.},
author = {Thirumalai, D and O'Brien, Edward P and Morrison, Greg and Hyeon, Changbong},
doi = {10.1146/annurev-biophys-051309-103835},
file = {:Users/rnowling/Documents/Mendeley Desktop/Thirumalai et al/2010/Theoretical Perspectives on Protein Folding/Thirumalai et al. - 2010 - Theoretical Perspectives on Protein Folding.pdf:pdf},
issn = {1936-1238},
journal = {Annual review of biophysics},
keywords = {molecular,role of protein length,single molecule force spectroscopy,transfer model,universality in protein folding},
month = feb,
pmid = {20192765},
title = {{Theoretical Perspectives on Protein Folding.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20192765},
year = {2010}
}
@article{Zuckerman2010,
abstract = {Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms?most of which are underpinned by a few key ideas?in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, due partly to the lack of widely used sampling measures. Expected final online publication date for the Annual Review of Biophysics Volume 40 is May 05, 2011. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.},
author = {Zuckerman, Daniel M},
doi = {10.1146/annurev-biophys-042910-155255},
file = {:Users/rnowling/Documents/Mendeley Desktop/Zuckerman/2010/Equilibrium Sampling in Biomolecular Simulations/Zuckerman - 2010 - Equilibrium Sampling in Biomolecular Simulations.pdf:pdf},
issn = {1936-1238},
journal = {Annual review of biophysics},
keywords = {algorithms,effective sample size,efficiency,hardware,timescales},
month = jul,
pmid = {21370970},
title = {{Equilibrium Sampling in Biomolecular Simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21370970},
year = {2010}
}
@article{Wilson1983,
author = {Wilson, E.L. and Itoh, T},
doi = {10.1016/0045-7949(83)90166-9},
file = {:Users/rnowling/Documents/Mendeley Desktop/Wilson, Itoh/1983/An eigensolution strategy for large systems/Wilson, Itoh - 1983 - An eigensolution strategy for large systems.pdf:pdf},
issn = {0045-7949},
journal = {Computers \& Structures},
number = {1-4},
pages = {259--265},
publisher = {Elsevier},
title = {{An eigensolution strategy for large systems}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0045794983901669},
volume = {16},
year = {1983}
}
@article{Bathe1980,
annote = {Describes methods, including overrelaxation of iteration vectors and shifting, for accelerating convergence of the Subspace Iteration (SSI) method.  Does not improve on computational cost of method.},
author = {Bathe, K.J. and Ramaswamy, S.},
doi = {10.1111/j.1525-139X.2011.00850.x},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bathe, Ramaswamy/1980/An accelerated subspace iteration method/Bathe, Ramaswamy - 1980 - An accelerated subspace iteration method.pdf:pdf},
issn = {0045-7825},
journal = {Computer Methods in Applied Mechanics and Engineering},
keywords = {Annotated,Diagonalization},
mendeley-tags = {Annotated,Diagonalization},
month = mar,
number = {3},
pages = {313--331},
pmid = {21517975},
publisher = {Elsevier},
title = {{An accelerated subspace iteration method}},
url = {http://linkinghub.elsevier.com/retrieve/pii/0045782580900122},
volume = {23},
year = {1980}
}
@article{Sameh2000,
author = {Sameh, Ahmed and Tong, Zhanye},
doi = {10.1016/S0377-0427(00)00391-5},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sameh, Tong/2000/The trace minimization method for the symmetric generalized eigenvalue problem/Sameh, Tong - 2000 - The trace minimization method for the symmetric generalized eigenvalue problem.pdf:pdf},
issn = {0377-0427},
journal = {Journal of computational and applied mathematics},
keywords = {davidson scheme,eigenvalue,eigenvector,jacobi,trace minimization},
month = nov,
number = {1-2},
pages = {155--175},
publisher = {Elsevier},
title = {{The trace minimization method for the symmetric generalized eigenvalue problem}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0377042700003915},
volume = {123},
year = {2000}
}
@article{Sameh1982,
author = {Sameh, A.H. and Wisniewski, J.A.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sameh, Wisniewski/1982/A Trace Minimization Algorithm for the Generalized Eigenvalue Problem/Sameh, Wisniewski - 1982 - A Trace Minimization Algorithm for the Generalized Eigenvalue Problem.pdf:pdf},
issn = {0036-1429},
journal = {SIAM Journal on Numerical Analysis},
number = {6},
pages = {1243--1259},
publisher = {JSTOR},
title = {{A Trace Minimization Algorithm for the Generalized Eigenvalue Problem}},
url = {http://www.jstor.org/stable/2157207},
volume = {19},
year = {1982}
}
@article{Tama2006,
abstract = {Computational studies of large macromolecular assemblages have come a long way during the past 10 years. With the explosion of computer power and parallel computing, timescales of molecular dynamics simulations have been extended far beyond the hundreds of picoseconds timescale. However, limitations remain for studies of large-scale conformational changes occurring on timescales beyond nanoseconds, especially for large macromolecules. In this review, we describe recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information. Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin.},
author = {Tama, Florence and Brooks, Charles L},
doi = {10.1146/annurev.biophys.35.040405.102010},
file = {:Users/rnowling/Documents/Mendeley Desktop/Tama, Brooks/2006/Symmetry, form, and shape guiding principles for robustness in macromolecular machines/Tama, Brooks - 2006 - Symmetry, form, and shape guiding principles for robustness in macromolecular machines.pdf:pdf},
issn = {1056-8700},
journal = {Annual review of biophysics and biomolecular structure},
keywords = {Algorithms,Computer Simulation,Macromolecular Substances,Macromolecular Substances: chemistry,Models, Chemical,Models, Molecular,Molecular Conformation,Molecular Motor Proteins,Molecular Motor Proteins: chemistry,Motion,Structure-Activity Relationship},
month = jan,
pages = {115--33},
pmid = {16689630},
title = {{Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16689630},
volume = {35},
year = {2006}
}
@proceedings{Porto97,
address = {Piscataway, NJ},
editor = {Porto, B},
publisher = {IEEE Press},
title = {{Proceedings of the IEEE International Conference on Evolutionary Computation}},
year = {1997}
}
@phdthesis{Cheng97,
annote = {Director-Gen, Mitsuo},
author = {Cheng, Runwei},
publisher = {Tokyo Institute of Technology},
title = {{Study on genetic algorithm-based optimal scheduling techniques}},
year = {1997}
}
@techreport{Cheng98,
author = {Cheng, Runwei and Gen, Mitsuo},
institution = {Ashikaga Institute of Technology},
title = {{A priority based encoding and shortest path problem}},
year = {1998}
}
@book{Cormen01,
author = {Cormen, Thomas H and Leiserson, Charles E and Rivest, Ronald L and Stein, Clifford},
publisher = {The MIT Press},
title = {{Introduction to Algorithms}},
year = {2001}
}
@book{EC2,
address = {Bristol, UK},
editor = {B\"{a}ck, Thomas and Fogel, David B and Michalewicz, Zbigniew},
isbn = {0-7503-0665-3},
publisher = {Institute of Physics Publishing},
title = {{Evolutionary Computation 2 - Advanced Algorithms and Operators}},
year = {2000}
}
@book{Papadimitriou98,
address = {Mineola, NY},
author = {Papadimitriou, Christos H and Steiglitz, Kenneth},
publisher = {Dover},
title = {{Combinatorial Optimization: Algorithms and Complexity}},
year = {1998}
}
@book{Eiben03,
address = {New York, NY},
author = {Eiben, A E and Smith, J E},
publisher = {Springer},
title = {{Introduction to Evolutionary Computation}},
year = {2003}
}
@thesis{Nowling10,
address = {St. Petersburg, FL, USA},
annote = {Describes Simulated Annealing and Genetic Algorithm metaheuristics for solving TSP, MKP, and MaxSAT.  Senior Thesis, Eckerd College},
author = {Nowling, Ronald James},
keywords = {Annotated,Optimization},
mendeley-tags = {Annotated,Optimization},
publisher = {Eckerd College},
title = {{Nature-inspired Metaheuristics for Combinatorial Optimization Problems}},
year = {2010}
}
@book{EC1,
address = {Bristol, UK},
editor = {B\"{a}ck, Thomas and Fogel, David B and Michalewicz, Zbigniew},
isbn = {0-7503-0664-5},
publisher = {Institute of Physics Publishing},
title = {{Evolutionary Computation 1 - Basic Algorithms and Operators}},
year = {2000}
}
@book{Russell03,
address = {Upper Saddle River, NJ},
author = {Russell, Stuart J and Norvig, Peter},
publisher = {Pearson Education, Inc.},
title = {{Artificial Intelligence: A Modern Approach}},
year = {2003}
}
@book{Gen00,
address = {New York, NY},
author = {Gen, Mitsuo and Cheng, Runwei},
publisher = {John Wiley and Sons},
title = {{Genetic Algorithms and Engineering Optimization}},
year = {2000}
}
@book{Goldberg89,
author = {Goldberg, D},
publisher = {Addison-Wesley},
title = {{Genetic Algorithms in Search, Optimization, and Machine Learning}},
year = {1989}
}
@article{Friedrichs2009,
author = {Friedrichs, M.S. and Eastman, Peter and Vaidyanathan, Vishal and Houston, Mike and Legrand, Scott and Beberg, A.L. and Ensign, D.L. and Bruns, C.M. and Pande, V.S.},
doi = {10.1002/jcc},
file = {:Users/rnowling/Documents/Mendeley Desktop/Friedrichs et al/2009/Accelerating molecular dynamic simulation on graphics processing units/Friedrichs et al. - 2009 - Accelerating molecular dynamic simulation on graphics processing units.pdf:pdf},
issn = {1096-987X},
journal = {Journal of Computational Chemistry},
keywords = {gpu,implicit solvent,molecular dynamics},
number = {6},
pages = {864--872},
publisher = {Wiley Online Library},
title = {{Accelerating molecular dynamic simulation on graphics processing units}},
url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.21209/full},
volume = {30},
year = {2009}
}
@article{Puchinger2009,
author = {Puchinger, Jakob and Raidl, Gunther R and Pferschy, Ulrich},
doi = {10.1287/ijoc.1090.0344},
file = {:Users/rnowling/Documents/Mendeley Desktop/Puchinger, Raidl, Pferschy/2009/The Multidimensional Knapsack Problem Structure and Algorithms/Puchinger, Raidl, Pferschy - 2009 - The Multidimensional Knapsack Problem Structure and Algorithms.pdf:pdf},
issn = {1091-9856},
journal = {INFORMS Journal on Computing},
keywords = {heuristics,history,integer linear programming,multidimensional knapsack problem,submitted march 2007},
month = aug,
number = {2},
pages = {250--265},
title = {{The Multidimensional Knapsack Problem: Structure and Algorithms}},
url = {http://joc.journal.informs.org/cgi/doi/10.1287/ijoc.1090.0344},
volume = {22},
year = {2009}
}
@article{Pisinger1995,
author = {Pisinger, David},
file = {:Users/rnowling/Documents/Mendeley Desktop/Pisinger/1995/Algorithms for knapsack problems/Pisinger - 1995 - Algorithms for knapsack problems.pdf:pdf},
journal = {DIKU, University of Copenhagen, Denmark, Diss},
title = {{Algorithms for knapsack problems}},
url = {http://www.diku.dk/OLD/publikationer/tekniske.rapporter/1995/95-1.ps.gz},
year = {1995}
}
@article{Knox1994,
author = {Knox, John Edward},
file = {:Users/rnowling/Documents/Mendeley Desktop/Knox/1994/Tabu search performance on the symmetric traveling salesman problem/Knox - 1994 - Tabu search performance on the symmetric traveling salesman problem.pdf:pdf},
journal = {Computers \& Operations Research},
number = {8},
pages = {867--876},
publisher = {Elsevier},
title = {{Tabu search performance on the symmetric traveling salesman problem}},
url = {http://www.sciencedirect.com/science/article/pii/0305054894900167},
volume = {21},
year = {1994}
}
@article{Pisinger2005,
author = {Pisinger, David},
doi = {10.1016/j.cor.2004.03.002},
file = {:Users/rnowling/Documents/Mendeley Desktop/Pisinger/2005/Where are the hard knapsack problems/Pisinger - 2005 - Where are the hard knapsack problems.pdf:pdf},
issn = {03050548},
journal = {Computers \& Operations Research},
keywords = {branch-and-bound,dynamic programming,knapsack problem,test instances},
month = sep,
number = {9},
pages = {2271--2284},
title = {{Where are the hard knapsack problems?}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S030505480400036X},
volume = {32},
year = {2005}
}
@article{Lin1973,
author = {Lin, S. and Kernighan, B.W.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Lin, Kernighan/1973/An effective heuristic algorithm for the traveling-salesman problem/Lin, Kernighan - 1973 - An effective heuristic algorithm for the traveling-salesman problem.pdf:pdf},
issn = {0030-364X},
journal = {Operations research},
number = {2},
pages = {498--516},
publisher = {JSTOR},
title = {{An effective heuristic algorithm for the traveling-salesman problem}},
url = {http://www.jstor.org/stable/169020},
volume = {21},
year = {1973}
}
@phdthesis{Knox1989,
author = {Knox, John Edward},
file = {:Users/rnowling/Documents/Mendeley Desktop/Knox/1989/The application of tabu search to the symmetric traveling salesman problem/Knox - 1989 - The application of tabu search to the symmetric traveling salesman problem.pdf:pdf},
title = {{The application of tabu search to the symmetric traveling salesman problem}},
url = {http://portal.acm.org/citation.cfm?id=916090},
year = {1989}
}
@article{Kirkpatrick1983,
abstract = {There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.},
annote = {Seminal paper describing Simulated Annealing, a metaheuristic modeled on metal annealing and statistical mechanics for solving combinatorial optimization problems.  Simulated Annealing allows moves against the optimization gradient determined by a probability distribution based on the current temperature, which is reduced according to a cooling or annealing schedule.},
author = {Kirkpatrick, S and Gelatt, C D and Vecchi, M P},
doi = {10.1126/science.220.4598.671},
file = {:Users/rnowling/Documents/Mendeley Desktop/Kirkpatrick, Gelatt, Vecchi/1983/Optimization by simulated annealing/Kirkpatrick, Gelatt, Vecchi - 1983 - Optimization by simulated annealing.pdf:pdf},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
keywords = {Annotated},
mendeley-tags = {Annotated},
month = may,
number = {4598},
pages = {671--80},
pmid = {17813860},
title = {{Optimization by simulated annealing.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17813860},
volume = {220},
year = {1983}
}
@article{Glover1990,
author = {Glover, Fred},
file = {:Users/rnowling/Documents/Mendeley Desktop/Glover/1990/Tabu search a tutorial/Glover - 1990 - Tabu search a tutorial.pdf:pdf},
issn = {0092-2102},
journal = {Interfaces},
pages = {74--94},
publisher = {JSTOR},
title = {{Tabu search: a tutorial}},
url = {http://www.jstor.org/stable/25061372},
year = {1990}
}
@article{Glover1990b,
author = {Glover, Fred},
file = {:Users/rnowling/Documents/Mendeley Desktop/Glover/1990/Tabu Search -- Part II/Glover - 1990 - Tabu Search -- Part II.pdf:pdf},
journal = {ORSA Journal on computing},
number = {1},
pages = {4--32},
title = {{Tabu Search -- Part II}},
url = {http://134.100.132.28/studentsatwork/literatur/sel\_glover\_b.pdf},
volume = {2},
year = {1990}
}
@article{Glover1990a,
author = {Glover, Fred},
file = {:Users/rnowling/Documents/Mendeley Desktop/Glover/1990/Tabu Search -- Part I/Glover - 1990 - Tabu Search -- Part I.pdf:pdf},
journal = {ORSA Journal on computing},
number = {1},
pages = {4--32},
title = {{Tabu Search -- Part I}},
url = {http://leeds-faculty.colorado.edu/glover/TS - Part II-ORSA-aw.pdf},
volume = {2},
year = {1990}
}
@inproceedings{Gen,
author = {Gen, Mitsuo and Cheng, Runwei and Wang, Dingwei},
booktitle = {Proceedings of 1997 IEEE International Conference on Evolutionary Computation (ICEC '97)},
doi = {10.1109/ICEC.1997.592343},
file = {:Users/rnowling/Documents/Mendeley Desktop/Gen, Cheng, Wang/1997/Genetic algorithms for solving shortest path problems/Gen, Cheng, Wang - 1997 - Genetic algorithms for solving shortest path problems.pdf:pdf},
isbn = {0-7803-3949-5},
pages = {401--406},
publisher = {Ieee},
title = {{Genetic algorithms for solving shortest path problems}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=592343},
year = {1997}
}
@article{Dorigo1997,
author = {Dorigo, Marco and Gambardella, Luca Maria},
doi = {10.1109/4235.585892},
file = {:Users/rnowling/Documents/Mendeley Desktop/Dorigo, Gambardella/1997/Ant colony system a cooperative learning approach to the traveling salesman problem/Dorigo, Gambardella - 1997 - Ant colony system a cooperative learning approach to the traveling salesman problem.pdf:pdf},
issn = {1089778X},
journal = {IEEE Transactions on Evolutionary Computation},
month = apr,
number = {1},
pages = {53--66},
title = {{Ant colony system: a cooperative learning approach to the traveling salesman problem}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=585892},
volume = {1},
year = {1997}
}
@article{Blum2003,
author = {Blum, Christian and Roli, Andrea},
file = {:Users/rnowling/Documents/Mendeley Desktop/Blum, Roli/2003/Metaheuristics in Combinatorial Optimization Overview and Conceptual Comparison/Blum, Roli - 2003 - Metaheuristics in Combinatorial Optimization Overview and Conceptual Comparison.pdf:pdf},
journal = {ACM Computing Surveys},
number = {3},
pages = {268--308},
title = {{Metaheuristics in Combinatorial Optimization : Overview and Conceptual Comparison}},
volume = {35},
year = {2003}
}
@article{Drexl1988,
author = {Drexl, A.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Drexl/1988/A simulated annealing approach to the multiconstraint zero-one knapsack problem/Drexl - 1988 - A simulated annealing approach to the multiconstraint zero-one knapsack problem.pdf:pdf},
journal = {Computing},
number = {1},
pages = {1--8},
publisher = {Springer},
title = {{A simulated annealing approach to the multiconstraint zero-one knapsack problem}},
url = {http://www.springerlink.com/index/P122185038368246.pdf},
volume = {40},
year = {1988}
}
@article{Chu1998,
author = {Chu, P.C. and Beasley, J.E.},
file = {:Users/rnowling/Documents/Mendeley Desktop/Chu, Beasley/1998/A genetic algorithm for the multidimensional knapsack problem/Chu, Beasley - 1998 - A genetic algorithm for the multidimensional knapsack problem.pdf:pdf},
issn = {1381-1231},
journal = {Journal of Heuristics},
number = {1},
pages = {63--86},
publisher = {Springer},
title = {{A genetic algorithm for the multidimensional knapsack problem}},
url = {http://www.springerlink.com/index/U7663408P38L03K2.pdf},
volume = {4},
year = {1998}
}
@article{Harvey2009,
author = {Harvey, M. J. and {De Fabritiis}, G.},
doi = {10.1021/ct900275y},
file = {:Users/rnowling/Documents/Mendeley Desktop/Harvey, De Fabritiis/2009/An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware/Harvey, De Fabritiis - 2009 - An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware.pdf:pdf},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
month = sep,
number = {9},
pages = {2371--2377},
title = {{An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware}},
url = {http://pubs.acs.org/doi/abs/10.1021/ct900275y},
volume = {5},
year = {2009}
}
@article{Sonnhammer2006,
author = {Sonnhammer, Erik L L and Wistrand, Markus and Ka, Lukas},
doi = {10.1110/ps.051745906.protein},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sonnhammer, Wistrand, Ka/2006/A general model of G protein-coupled receptor sequences and its application to detect remote homologs/Sonnhammer, Wistrand, Ka - 2006 - A general model of G protein-coupled receptor sequences and its application to detect remote homologs.pdf:pdf},
journal = {Protein Science},
keywords = {g protein-coupled receptors,gpcrs,hidden markov model,large and diverse superfamily,make up a,of transmembrane,org,protein classification,proteinscience,see www,supplemental material,the g protein-coupled receptors,tm},
pages = {509--521},
title = {{A general model of G protein-coupled receptor sequences and its application to detect remote homologs}},
year = {2006}
}
@article{Grimmelikhuijzen2007,
author = {Grimmelikhuijzen, Cornelis J P and Cazzamali, Giuseppe and Williamson, Michael and Hauser, Frank},
doi = {10.1002/ps},
file = {:Users/rnowling/Documents/Mendeley Desktop/Grimmelikhuijzen et al/2007/The promise of insect genomics/Grimmelikhuijzen et al. - 2007 - The promise of insect genomics.pdf:pdf},
journal = {Pest Management Science},
number = {July 2006},
pages = {413--416},
title = {{The promise of insect genomics}},
volume = {416},
year = {2007}
}
@article{Morcos2010,
author = {Morcos, Faruck and Chatterjee, Santanu and McClendon, Christopher L. and Brenner, Paul R. and L\'{o}pez-Rend\'{o}n, Roberto and Zintsmaster, John and Ercsey-Ravasz, Maria and Sweet, Christopher R. and Jacobson, Matthew P. and Peng, Jeffrey W. and Izaguirre, Jes\'{u}s a.},
doi = {10.1371/journal.pcbi.1001015},
editor = {Nussinov, Ruth},
file = {:Users/rnowling/Documents/Mendeley Desktop/Morcos et al/2010/Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW/Morcos et al. - 2010 - Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Computational Biology},
month = dec,
number = {12},
pages = {e1001015},
title = {{Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1001015},
volume = {6},
year = {2010}
}
@article{Schuyler2004,
abstract = {The ability to infer dynamic motions from an equilibrium (static) conformation of a protein can be essential in establishing structure-function relationships. In particular, the low-frequency motions are of functional interest because statistical mechanics predicts these motions will have the largest amplitudes. In this paper, we address the computational cost of normal mode analysis (NMA) applied to a C(alpha)-based elastic network model (C(alpha)-NMA) and present a new coarse-grained rigid-body-based analysis (cluster-NMA). This new method represents a protein as a collection of rigid bodies interconnected with harmonic potentials. This representation produces reduced degree-of-freedom (DOF) equations of motion (EOMs) which, even in the case of large structures (10(3+) residues), enables the computation of normal modes to be done on a desktop PC. We present the complete theory and analysis of cluster-NMA and also include its application to a variety of structures. The results of the new method are compared with C(alpha)-NMA and it is shown that cluster-NMA produces very good approximations to the lowest modes at a fraction of the computational cost.},
author = {Schuyler, Adam D and Chirikjian, Gregory S},
doi = {10.1016/S1093-3263(03)00158-X},
file = {:Users/rnowling/Documents/Mendeley Desktop/Schuyler, Chirikjian/2004/Normal mode analysis of proteins a comparison of rigid cluster modes with C(alpha) coarse graining/Schuyler, Chirikjian - 2004 - Normal mode analysis of proteins a comparison of rigid cluster modes with C(alpha) coarse graining.pdf:pdf},
issn = {1093-3263},
journal = {Journal of molecular graphics \& modelling},
keywords = {Algorithms,Amino Acid Sequence,Amino Acids,Amino Acids: chemistry,Chaperonin 10,Chaperonin 10: chemistry,Chaperonin 60,Chaperonin 60: chemistry,Cluster Analysis,Computational Biology,Computational Biology: economics,Computational Biology: methods,Lactoferrin,Lactoferrin: chemistry,Models, Statistical,Models, Theoretical,Motion,Protein Conformation,Protein Structure, Secondary,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Time Factors},
month = jan,
number = {3},
pages = {183--93},
pmid = {14629977},
title = {{Normal mode analysis of proteins: a comparison of rigid cluster modes with C(alpha) coarse graining.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14629977},
volume = {22},
year = {2004}
}
@article{Fredriksson2005,
author = {Fredriksson, Robert and Schi\"{o}th, H.B.},
doi = {10.1124/mol.104.009001.sequenced},
file = {:Users/rnowling/Documents/Mendeley Desktop/Fredriksson, Schi\"{o}th/2005/The repertoire of G-protein–coupled receptors in fully sequenced genomes/Fredriksson, Schi\"{o}th - 2005 - The repertoire of G-protein–coupled receptors in fully sequenced genomes.pdf:pdf},
journal = {Molecular pharmacology},
number = {5},
pages = {1414},
publisher = {ASPET},
title = {{The repertoire of G-protein–coupled receptors in fully sequenced genomes}},
url = {http://molpharm.aspetjournals.org/content/67/5/1414.short},
volume = {67},
year = {2005}
}
@article{Schuyler2005,
abstract = {The structure-function relationship is critical to understanding the biologically relevant functions of protein structures. Various experimental techniques and numerical modeling methods, normal mode analysis (NMA) in particular, have been employed to gain insight into this relationship. Experimental methods are often unable to provide all the desired information and comprehensive modeling techniques are often too computationally expensive. The authors build upon and optimize their cluster normal mode analysis (cNMA) tool, which uses embedded rigid-bodies and harmonic potentials to capture the biologically significant, low-frequency, oscillations of protein structures. cNMA represents atomic details with a scalable number of degrees-of-freedom, which can be chosen independent of structure size. This representation overcomes the otherwise quadratic order memory requirements and cubic order computational complexity associated with traditional all-atom NMA. cNMA is two orders of magnitude faster than traditional all-atom NMA when clustering by residue (very high resolution) and in the more traditional application using a fixed number of clusters, cNMA computationally scales as O(n), which is two orders of complexity faster than all-atom NMA. cNMA is presented and very large example structures with up to 10(6) atoms are analyzed on a notebook PC in the time scale of minutes/hours. The resulting mode shapes help identify biologically significant, conformational pathways.},
annote = {Coarse-grained NMA which allows clusters of atoms to be defined arbitrarily.  Uses reduced spaced where coordinates conform to rotation and translation to represent vectors rather than Cartesian space.},
author = {Schuyler, Adam D and Chirikjian, Gregory S},
doi = {10.1016/j.jmgm.2005.05.002},
file = {:Users/rnowling/Documents/Mendeley Desktop/Schuyler, Chirikjian/2005/Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA/Schuyler, Chirikjian - 2005 - Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA.pdf:pdf},
issn = {1093-3263},
journal = {Journal of molecular graphics \& modelling},
keywords = {Cluster Analysis,Computational Biology,Computational Biology: methods,Protein Structure, Tertiary,Proteins,Proteins: chemistry,Structure-Activity Relationship},
month = sep,
number = {1},
pages = {46--58},
pmid = {15990344},
title = {{Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15990344},
volume = {24},
year = {2005}
}
@article{Ghysels2009,
author = {Ghysels, A N and Speybroeck, Veronique V A N and Pauwels, Ewald and Catak, Saron and Brooks, Bernard R and Neck, Dimitri V A N and Waroquier, Michel},
doi = {10.1002/jcc},
file = {:Users/rnowling/Documents/Mendeley Desktop/Ghysels et al/2009/Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians/Ghysels et al. - 2009 - Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians.pdf:pdf},
journal = {Journal of Computational Chemistry},
keywords = {Diagonalization,NMA,cinchona,hessian,lao binding protein,mbh,mobile block hessian,nma,normal modes,partial hessian,partial optimization,phva,rtb,vibrational modes,vibrational subsystem analysis,vsa},
mendeley-tags = {Diagonalization,NMA},
title = {{Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians}},
year = {2009}
}
@article{Sedeh2009,
annote = {Application of SSI to protein NMA.  Utilize linear progression of eigenvalues to find number of subspace vectors and iterations to optimize run time of SSI.  Further speed ups produced by using previously computed modes as basis for subspace in SSI.},
author = {Sedeh, Reza Sharifi and Bathe, Mark},
doi = {10.1002/jcc},
file = {:Users/rnowling/Documents/Mendeley Desktop/Sedeh, Bathe/2009/The Subspace Iteration Method in Protein Normal Mode Analysis/Sedeh, Bathe - 2009 - The Subspace Iteration Method in Protein Normal Mode Analysis.pdf:pdf},
journal = {Journal of Computational Chemistry},
keywords = {Annotated,Diagonalization,NMA,conformational change pathway,frequency,macromolecule,mode shape},
mendeley-tags = {Annotated,Diagonalization,NMA},
title = {{The Subspace Iteration Method in Protein Normal Mode Analysis}},
year = {2009}
}
@article{Nowling2011,
abstract = {NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.},
annote = {Describes data model and application for converting NMR data between differen file formats.},
author = {Nowling, Ronald J and Vyas, Jay and Weatherby, Gerard and Fenwick, Matthew W and Ellis, Heidi J C and Gryk, Michael R},
doi = {10.1007/s10858-011-9497-1},
file = {:Users/rnowling/Documents/Mendeley Desktop/Nowling et al/2011/CONNJUR spectrum translator an open source application for reformatting NMR spectral data/Nowling et al. - 2011 - CONNJUR spectrum translator an open source application for reformatting NMR spectral data.pdf:pdf},
issn = {1573-5001},
journal = {Journal of biomolecular NMR},
keywords = {Annotated,connjur,conversion,fid,reconstruction,software,spectrum},
mendeley-tags = {Annotated},
month = mar,
pmid = {21409563},
title = {{CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21409563},
year = {2011}
}
@article{Gookin2008,
abstract = {BACKGROUND: The classic paradigm of heterotrimeric G-protein signaling describes a heptahelical, membrane-spanning G-protein coupled receptor that physically interacts with an intracellular G alpha subunit of the G-protein heterotrimer to transduce signals. G-protein coupled receptors comprise the largest protein superfamily in metazoa and are physiologically important as they sense highly diverse stimuli and play key roles in human disease. The heterotrimeric G-protein signaling mechanism is conserved across metazoa, and also readily identifiable in plants, but the low sequence conservation of G-protein coupled receptors hampers the identification of novel ones. Using diverse computational methods, we performed whole-proteome analyses of the three dominant model plant species, the herbaceous dicot Arabidopsis thaliana (mouse-eared cress), the monocot Oryza sativa (rice), and the woody dicot Populus trichocarpa (poplar), to identify plant protein sequences most likely to be GPCRs. RESULTS: Our stringent bioinformatic pipeline allowed the high confidence identification of candidate G-protein coupled receptors within the Arabidopsis, Oryza, and Populus proteomes. We extended these computational results through actual wet-bench experiments where we tested over half of our highest ranking Arabidopsis candidate G-protein coupled receptors for the ability to physically couple with GPA1, the sole G alpha in Arabidopsis. We found that seven out of eight tested candidate G-protein coupled receptors do in fact interact with GPA1. We show through G-protein coupled receptor classification and molecular evolutionary analyses that both individual G-protein coupled receptor candidates and candidate G-protein coupled receptor families are conserved across plant species and that, in some cases, this conservation extends to metazoans. CONCLUSION: Our computational and wet-bench results provide the first step toward understanding the diversity, conservation, and functional roles of plant candidate G-protein coupled receptors.},
author = {Gookin, Timothy E and Kim, Junhyong and Assmann, Sarah M},
doi = {10.1186/gb-2008-9-7-r120},
file = {:Users/rnowling/Documents/Mendeley Desktop/Gookin, Kim, Assmann/2008/Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar computational prediction and in-vivo protein coupling/Gookin, Kim, Assmann - 2008 - Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar computational prediction and in-vivo protein coupling.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
keywords = {Amino Acid Sequence,Arabidopsis,Arabidopsis Proteins,Arabidopsis Proteins: chemistry,Arabidopsis Proteins: classification,Arabidopsis Proteins: metabolism,Arabidopsis: metabolism,Computational Biology,Computational Biology: methods,GTP-Binding Protein alpha Subunits,GTP-Binding Protein alpha Subunits: metabolism,Molecular Sequence Data,Oryza sativa,Oryza sativa: genetics,Oryza sativa: metabolism,Phylogeny,Plant Proteins,Plant Proteins: chemistry,Plant Proteins: classification,Plant Proteins: metabolism,Populus,Populus: genetics,Populus: metabolism,Proteome,Proteome: chemistry,Receptors, G-Protein-Coupled,Receptors, G-Protein-Coupled: chemistry,Receptors, G-Protein-Coupled: classification,Receptors, G-Protein-Coupled: metabolism,Sequence Analysis, Protein,Sequence Homology, Amino Acid},
month = jan,
number = {7},
pages = {R120},
pmid = {18671868},
title = {{Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18671868},
volume = {9},
year = {2008}
}
@article{Freville2004,
author = {Freville, Arnaud},
doi = {10.1016/S0377-2217(03)00274-1},
file = {:Users/rnowling/Documents/Mendeley Desktop/Freville/2004/The multidimensional 0-1 knapsack problem An overview/Freville - 2004 - The multidimensional 0-1 knapsack problem An overview.pdf:pdf},
issn = {0377-2217},
journal = {European Journal of Operational Research},
keywords = {1 knapsack problem,branch-and-bound algorithms,heuristics,ing,multidimensional 0,preprocess-,probabilistic and worst-case analysis,surrogate duality},
month = may,
number = {1},
pages = {1--21},
publisher = {Elsevier},
title = {{The multidimensional 0-1 knapsack problem: An overview}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0377221703002741},
volume = {155},
year = {2004}
}
@article{Hsu2003,
address = {New York, New York, USA},
author = {Hsu, Chung-Hsing and Kremer, Ulrich},
doi = {10.1145/781136.781137},
file = {:Users/rnowling/Documents/Mendeley Desktop/Hsu, Kremer/2003/The design, implementation, and evaluation of a compiler algorithm for CPU energy reduction/Hsu, Kremer - 2003 - The design, implementation, and evaluation of a compiler algorithm for CPU energy reduction.pdf:pdf},
isbn = {1581136625},
journal = {Proceedings of the ACM SIGPLAN 2003 conference on Programming language design and implementation - PLDI '03},
keywords = {dynamic voltage scaling,energy savings},
pages = {38},
publisher = {ACM Press},
title = {{The design, implementation, and evaluation of a compiler algorithm for CPU energy reduction}},
url = {http://portal.acm.org/citation.cfm?doid=781131.781137},
year = {2003}
}
@article{Skeel2007,
author = {Skeel, Robert D},
file = {:Users/rnowling/Documents/Mendeley Desktop/Skeel/2007/Computational Methods for Molecular Simulations/Skeel - 2007 - Computational Methods for Molecular Simulations.pdf:pdf},
title = {{Computational Methods for Molecular Simulations}},
year = {2007}
}
@book{Saad2011,
author = {Saad, Yousef},
edition = {2},
file = {:Users/rnowling/Documents/Mendeley Desktop/Saad/2011/Numerical Methods for Large Eigenvalue Problems/Saad - 2011 - Numerical Methods for Large Eigenvalue Problems.pdf:pdf},
isbn = {0719033861},
publisher = {Manchester Univ Pr},
title = {{Numerical Methods for Large Eigenvalue Problems}},
url = {http://books.google.com/books?hl=en\&amp;lr=\&amp;id=FAkNAQAAIAAJ\&amp;oi=fnd\&amp;pg=PP15\&amp;dq=Numerical+Methods+for+Large+Eigenvalue+Problems\&amp;ots=IO\_l8kh8BG\&amp;sig=VMd\_wzdGahK-NUHld32CpHjtbqs},
year = {2011}
}
@inproceedings{Nowling2011a,
annote = {Describes new encoding scheme that can be used to solve permutation and constraint problems with general Simulated Annealing and Genetic Algorithm frameworks and in some cases, makes those problems easier to solve.},
author = {Nowling, Ronald J and Mauch, Holger},
booktitle = {Information Technology -- New Generations},
file = {:Users/rnowling/Documents/Mendeley Desktop/Nowling, Mauch/2011/Priority Encoding Scheme for Solving Permutation and Constraint Problems with Genetic Algorithms and Simulated Annealing/Nowling, Mauch - 2011 - Priority Encoding Scheme for Solving Permutation and Constraint Problems with Genetic Algorithms and Simulated Annealing.pdf:pdf},
keywords = {Annotated},
mendeley-tags = {Annotated},
title = {{Priority Encoding Scheme for Solving Permutation and Constraint Problems with Genetic Algorithms and Simulated Annealing}},
year = {2011}
}
@article{Liu2008,
author = {Liu, Xiaolan and Mauch, Holger and Hao, Zhifeng and Wu, Guangchao},
doi = {10.1109/ICBBE.2008.171},
file = {:Users/rnowling/Documents/Mendeley Desktop/Liu et al/2008/A Compounded Genetic and Simulated Annealing Algorithm for the Closest String Problem/Liu et al. - 2008 - A Compounded Genetic and Simulated Annealing Algorithm for the Closest String Problem.pdf:pdf},
isbn = {978-1-4244-1747-6},
journal = {2008 2nd International Conference on Bioinformatics and Biomedical Engineering},
keywords = {-closest string problem,A Compounded Genetic and Simulated Annealing Algor,computational biology,genetic algorithm,hybrid methods,simulated annealing},
month = may,
number = {1},
pages = {702--705},
publisher = {Ieee},
title = {{A Compounded Genetic and Simulated Annealing Algorithm for the Closest String Problem}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4535051},
year = {2008}
}
@inproceedings{Ellis2011,
annote = {Describes how prototyping was used to understand how to develop an application for the very complex domain of NMR data processing, where the most appropriate software architecture and user interface models have not yet been identified},
author = {Ellis, Heidi J C and Nowling, Ronald J and Vyas, Jay and Martyn, Timothy O and Gryk, Michael R},
booktitle = {Information Technology -- New Generations},
file = {:Users/rnowling/Documents/Mendeley Desktop/Ellis et al/2011/Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins/Ellis et al. - 2011 - Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins.pdf:pdf},
keywords = {Annotated,bioinformatics,integration,nmr},
mendeley-tags = {Annotated},
title = {{Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins}},
year = {2011}
}
@article{Suzuki1998,
author = {Suzuki, Joe},
file = {:Users/rnowling/Documents/Mendeley Desktop/Suzuki/1998/A Further Result on the Markov Chain Model of Genetic Algorithms and Its Application to a Simulated Annealing-Like Strategy/Suzuki - 1998 - A Further Result on the Markov Chain Model of Genetic Algorithms and Its Application to a Simulated Annealing-Like Strategy.pdf:pdf},
issn = {1083-4419},
journal = {Systems, Man, and Cybernetics, Part B: Cybernetics, IEEE Transactions on},
number = {1},
pages = {95--102},
publisher = {IEEE},
title = {{A Further Result on the Markov Chain Model of Genetic Algorithms and Its Application to a Simulated Annealing-Like Strategy}},
url = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=658583},
volume = {28},
year = {1998}
}
@article{Suzuki1995,
author = {Suzuki, Joe},
doi = {10.1109/21.370197},
file = {:Users/rnowling/Documents/Mendeley Desktop/Suzuki/1995/A Markov chain analysis on simple genetic algorithms/Suzuki - 1995 - A Markov chain analysis on simple genetic algorithms.pdf:pdf},
issn = {00189472},
journal = {IEEE Transactions on Systems, Man, and Cybernetics},
month = apr,
number = {4},
pages = {655--659},
title = {{A Markov chain analysis on simple genetic algorithms}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=370197},
volume = {25},
year = {1995}
}
@article{Rudolph1994,
abstract = {This paper analyzes the convergence properties of the canonical genetic algorithm (CGA) with mutation, crossover and proportional reproduction applied to static optimization problems. It is proved by means of homogeneous finite Markov chain analysis that a CGA will never converge to the global optimum regardless of the initialization, crossover, operator and objective function. But variants of CGA's that always maintain the best solution in the population, either before or after selection, are shown to converge to the global optimum due to the irreducibility property of the underlying original nonconvergent CGA. These results are discussed with respect to the schema theorem.},
author = {Rudolph, Gunter},
doi = {10.1109/72.265964},
file = {:Users/rnowling/Documents/Mendeley Desktop/Rudolph/1994/Convergence analysis of canonical genetic algorithms/Rudolph - 1994 - Convergence analysis of canonical genetic algorithms.pdf:pdf},
issn = {1045-9227},
journal = {IEEE transactions on neural networks / a publication of the IEEE Neural Networks Council},
keywords = {canonical genetic algorithm,global convergence,markov chains,schema theorem},
month = jan,
number = {1},
pages = {96--101},
pmid = {18267783},
title = {{Convergence analysis of canonical genetic algorithms.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18267783},
volume = {5},
year = {1994}
}
@article{Bathe1973,
annote = {Presentes Subspace Iteration (SSI) method for approximating the p smallest eigenpairs of a matrix using a set of q randomly chosen, linearly independent vectors. Performance can be optimized by choosing q accordingly. Requires knowing matrix inverse.},
author = {Bathe, Klaus-J\"{u}rgen and Wilson, Edward L.},
doi = {10.1002/nme.1620060207},
file = {:Users/rnowling/Documents/Mendeley Desktop/Bathe, Wilson/1973/Solution methods for eigenvalue problems in structural mechanics/Bathe, Wilson - 1973 - Solution methods for eigenvalue problems in structural mechanics.pdf:pdf},
issn = {0029-5981},
journal = {International Journal for Numerical Methods in Engineering},
keywords = {Annotated,Diagonalization},
mendeley-tags = {Annotated,Diagonalization},
number = {2},
pages = {213--226},
title = {{Solution methods for eigenvalue problems in structural mechanics}},
url = {http://doi.wiley.com/10.1002/nme.1620060207},
volume = {6},
year = {1973}
}
